I've seen a number of fangames and romhacks that seek to emulate anime-like concepts and I have a few suggestions to offer that would be worth mentioning to work with this if at all possible.
1: Evolving during a battle: I've seen two Essentials fangames do this, in that a pokemon when they meet the level up condition (friendship also technically counts in this considering) they evolve during the battle currently being waged. This sometimes is a bit buggy however in cases with cancelling evolution manually but oing this can make a story battle against an evil team appear more meaningful if you have a starter evolve during a battle with an admin or evil team boss.
Thank you so much for your comment :)
It is something that we are trying to implement, so far it has been very difficult, because using EBS + Following Pokemon has made things very difficult ... But we keep trying, it is one of the things we would not want to put aside.
2: Event pokemon: There was one fangame I remember that had special examples of certain pokemon which are central to a story arc that one could obtain. In a situation like this if you're able to do it, it'd be cool to have them evolve in scripted events be they a minigame or a cutscene where the overworld sprites "battle" (as opposed to actually entering a battle) leading to an evolution. Said evolution cannot be triggered under normal means until this point. To add to their uniqueness they could have moves and abilities which are decidedly not possible to learn for that species, or normally would require a long sequence of chain breeding to obtain.
We were thinking about it as an option, the point is that we are quite interested in not ruining the gaming experience due to the fact that we embrace the world of anime. We would like the player to enjoy the experience by having the team that most wants to put together and not having to follow the anime to the letter. No doubt there are many events, places and episodes that are activated if you have a certain Pokemon in your team (For example, decide if you want to let your BUTTERFREE migrate in spring) and other events that will be a bit more permissive (For example, if In the anime something depends on BULBASAUR, we want you to live the experience also if you already have an IVYSAUR or VENUSAUR in your team)...
We want to be able to adapt everything as well as possible, but without forget that our guide is also the experience of the original game. But it is an option :)
3: This is less about story but more on mechanics. The fangame pokemon Radiant had a different way Hidden Power worked in that allowed one to get hidden power to work based on the species as opposed to IVs. This would more than likely be really difficult to do here however so something I would suggest is getting Hidden Power as soon as you can get your starter, and the person who gives it to you can tell you the hidden power. Or at least have a readout on the stat window telling you a pokemon's hidden power to eliminate the middle man altogether.
This is something we had not thought about and can certainly be a good contribution. The three starters of Kanto can be obtained in the game by doing various missions, that moment would be a good useful option. :)
Thank you for all the help, and sorry about my english!