Disclaimer - my entire knowledge of pokemon is based on my having watched the first series of the cartoon when I was about eleven or twelve, which is over ten yeras ago now.

Pokemon biology ... yeah. I can't really say much on the front of the mechanics of Pokeballs or of the whole laser thing, but as for the 'evolution' ... well. There are things I can say on that score.

Evolution, for a start, is the wrong term. Metamorphosis is the correct term. Yes, that's right, what butterflies do. I know there are different types of Pokemon and that only some of them are 'insect type', but if I had to fit them into an Earth phylogenetic system I would put them in the phylum Arthropoda.

Yes, I *know* some of them are mammal-like and rock-like and plant-like, but hear me out :)

See, the thing about arthropods (not just insects, but we'll get to the classification thing soon, I promise) is that they are incredible mimics. There are arthropods that are almost impossible to distinguish from bits of plant, from bits of stone, from snakes and so forth. And arthropods metamorphose, which is very important.

Animals and plants are grouped based on different charactersitics, and the idea of grouping them is to make sure that each group contains only organisms that are more closely related to each other than they are to everything outside the group. And modes of life are very important criteria for dividing up organisms - outward appearance is actually one of the least important criteria - it is so easily changed by selection pressure. So given that all Pokemon have this same basic mode of reproduction/metamorphosis, which can be catalysed by rocks, of all things (and I'll get onto THAT later as well), I'm going to group them in their own class, part of the phylum Arthropoda and a sister-taxon to the classes Insecta, Chelicerata etc etc. This group is cladistically correct because it is monophyletic (nothing that belongs in the group has been left out - no other animals reproduce like Pokemon do)

As for the rock catalyst thing, it is possible (not probable, and not likely, but possible) that these magical rocks contain essential elements or compounds that catalyse the chemical processes that cause them to metamorphose, or that stress them into changing, somewhat like bad water conditions force axolotls (which are normally neotenous and happy about it) to undergo the last stage of development and become newts.
This is a poor and depauperate explanation but I'm sort of scraping the bottom of the barrel here.

I would like to state that this is me mostly me waffling on about biology and probably mostly talking out my arse and that I claim no authority on Pokemon canon. That said ... if these ideas are any use, feel free to use them.

Since it is aimed at children, the characters don't age so that they can continue to connect with their audience. Other anime that is set over a long period of time (many anime aren't) do have characters that age. One example is Dragonball. The main character started the series as 12, but by the end of GT he's in his 60s with grandchildren (even if he does age spectacularily well).

As for the other stuff... It's a children's show. It doesn't need logic. The manga might have more detail though, I think that was aimed at an older audience.

Yeah, I was wondering about where the water would come from for the move surf. If they pull from the environment then does that mean that they can't use it if they are in a desert? I gave up analyzing it. You just have to be creative when you write and try to work around it.

http://tvtropes.org/pmwiki/pmwiki.php/Main/HotSkittyOnWailordAction

Pokemon doesn't have many canon explanations for these, as a reuslt, some of them are often left to the fandom to decide. A lot of these are also assumptions and guesses on my part to apply logic to the world.

First paragraph: It's a show aimed at kids mostly, same as the games. Characters don't look 10, but rather cna fit into most early age brackets. And yes, Pokemon is anime.

There is no logical explanation behind Pokeballs, other than the diffusion of matter. In my stories, the Pokeball contains technology capable of transferring physical matter into a pure energy form, thus allowing the Pokemon to be stored within the Pokeball. As all amtter is simply different forms of energy, the conversion is easy enough to say in theory, but hard ot put into practice. Additionally, Pokeballs can expand or reduce in size due to the technology of the Pokeball moving around, thus allowing it to enter a more compact mode. It's unsure what the inside of a Pokeball is like, seeing as the being inside is theoretically pure energy, but it is often guessed, and supported by Nintendo, that the inside of the Pokeball varies to give the mind of the Pokemon, or the physical body if the energy process turns it to energy, then to matter again inside the Pokeball, a more sane level of existance. A water type may need water, thus the Pokeball compensates thruogh inbuilt technology. In this thread, of the inside of a Pokeball is chosen to suit the Pokemon, it also follows that the environment is suitable for the Pokemon to rest and heal. Given the choice, I suppose a Pokemon may even be able to listen to events occuring outside its Pokeball, giving the possibility that the Pokeball has psychic capabilities and responds to the thoughts of a Pokemon.
Within the anime and games, Pokemon do need additional medicine for particularly extreme wounds or conditions (Poisoned, as an example), but other than that, Pokemon have probably developed accelerated healing abilities as a result of their frequent practice of battling. Pokemon have aso been shown to be fed regularly outside of the Pokeball, showing that the Pokeball doesn't seem to provide nutrition. As a result, they can starve to death unless they are Ghost Types.

Pokemon do not evolve constantly, as each tends to have one, or at most, two forms to evolve into. Humans are constantly evolving in their childhood to their teenage, and then adult forms, it's just more gradual. In the case of Pokemon, these changes are more sudden. It's the training that allows a Pokemon to evolve, similar to how exercise and nutrition allows the human body to grow towards adulthood. It's quite similar to the human developement, just occurs at set stages that can spontaneously happen, whether upon an emotion trigger or the need to evolve to deal with their current situation (See when Ash's Charmeleon evolved to Charizard to save Ash from the Aerodactyl). The elemental stones are shown to contain concentrated doses of whatever element they represent, which leads to the suggestion of radioactivity, a natural element not found on earth or even divine blessing.
Eevee is capable of evolving because it is very adaptable. It has been specifically noted that Eevee's DNA is unstable, allowing it to potentially absorb part of the environment around it and evolve to best suit it. This would explain why Eevee evolves around the Ice Rock in Diamond and Pearl, or to Vaporean when exposed to a Water Stone.

Pokemon attacks can be a bit tricky, but again, I also dealt with this in my own Pokemon fanfic. The water used by certain water Pokemon (Squirtle, Totodile, Mudkip, etc) is developed in an internal water pouch which frequently fills with either excess saliva, stomach acid (Explaining why several Water Types are also poison types), or is capable of combining oxygen in the air with hydrogen produced naturally by the body.
Leaves and vines are harder to explain. However, there are cases where plants can be quite effective against regular metal. Theoretically, by binding together thousands of paper thin layers of membrane, you can create a substance equal in power to steal. This would be seal in a laquer naturally product by grass Pokemon. The vines may simply be the result of seeds carried by the Pokemon being forced to grow rapidly, or even the Grass Pokemon itself forcing its body to grow by concentrating sunlight, nutrients and water in its body to force the growth or attack (Solarbeam requires sunlight to fire, etc).

And that's all stuff I've dealt with in my story. It's actually quite fun, applying logic, you just gotta ask 'How can this work', and then create the theories. I dealt with the paradox of 'Pokemon fire = Not Death' vs 'Building on Fire = Death' by saying that fire types excrete a natural chemical in their fire sacs which limits the heat their flames can reach.

I, personally, gave up on logic in Pokemon a long time ago. I don't think it's meant to make sense, but just to entertain. It's a fantasy world with different rules etc.

Lights etc are just visual effects, for the viewers, in my opinion. Kids are attracted by shiny things.

Evolution could just be a case of 'I'm too powerful/experienced for this form now, I need to be at the next one to continue getting stronger.' There are exceptions, of course (i.e. Ash/Satoshi's Pikachu and its ability to defeat almost anything), but most things evolve once they're strong enough. I believe it was mentioned somewhere, perhaps in the Pokedex of one of the games, that Eevee has an unstable genetic code and therefore can evolve into whatever Pokemon is attuned to the stone you use on it (about seven or so now I think).

People do age in anime, most of the time, but Pokemon is just weird with its non-aging. The Digimon Adventures 01 characters were older by the time of 02, to use your other mon-anime example. Bleach, Gundam 00, Naruto, Code Geass and Ouran all show the characters aging, whether through time skips to the future or flashbacks to the past.

Good luck with figuring out Pokemon logic and science.