Ah Mega Evolution, it was a wonderful thing when it first came out so fresh and added a whole new depth to competitive battling but it's kinda sad when pokemon who really deserve it never get one, i'm glad to see you have an idea for making Custom Mega's so i'm interested to see how it turns out.
Following pokemon was a feature pokemon loved but it never returned in later pokemon games, though it's been added into Fan-Games it's a nice little feature, Though if your going to add it into the game could it be optional to turn it off either via the options menu or through a button of the keyboard?
When Gen 2 came out having a second region was an awesome concept you got to travel to another region and have a whole new adventure which added a massive amount of gameplay. Having multiple regions is a nice idea. Though will it be in one adventure or two? by that i mean will for example you get to say level 60 by the champion in the first region and then 90+ by the time you finish the second region or will you have your first region and when you gain access to the second it's an entirely new adventure where you pick a level 5 starter and do it all over again?
Pokemon games have always had a vast portion of stuff set on the main land to the game, however Hoenn for example had a large section of water with plenty of places you could surf and use dive it adds more area's to explore and even be useful for hiding things such as mega stones or side quest's of some sort maybe locations with rare pokemon i like the idea of having more to explore and possibly have rare items or pokemon hidden away.
Shadow pokemon were a unique introduction in the Gamecube games it's an interesting little feature however as long as there's a way to catch the ones that you've missed then go for it, because it'd be annoying if it ko'd itself from recoil or something and you never had a chance to rebattle it.
The Battle Frontier was a lot of fun in Emerald and Gen 4, it added several places in which you could flex your skills on competitive battling in unique ways adding a whole new fun factor about battles, the chance to earn the Symbol from the facility gave you all the more reason to keep trying. I'm interested to see if you add the Hoenn or Sinnoh frontier or even both, maybe make your own facilities, Personally i'd like if you did both. The battle tower is a classic go as far as you can, the Battle Factory with renting pokemon added a certain luck factor for getting a good variety on your team. the Battle Pyramid was probably the most challenging of all facilities for me personally probably because i rage quit for it being to difficult all those years ago but i'd love to see it Re-amped in Gen 6 mechanics. The Battle Arcade was a unique roulette style battle system which was in reality a horrible way to rely on RNG but on the other hand it was such a unique experience it was actually fun. The Battle Castle being point based had a cool little idea of you being able to buy support it's kinda like softcore version of the Pyramid which i really liked. The Battle Hall has got to be one of my favourite places being able to face pokemon in a difficulty level of 1-9 in each respective type was a really unique way to battle i really liked the concept of it. And all the other facilities i didn't mention would also be nice to add into your game since they're all a diverse way to battle it'd make great gameplay value under 6th Gen mechanics
The pokemon world tournament was another one of my favourite features within the pokemon games, the Nostalgia of facing regional gym leaders and champions was a lot of fun, and being able to face more competitive Monotype teams was also really fun. Personally i find Monotype a lot of fun to play in terms of competitive battles, I would really love to see the PWT make a return in your game with the classic Gym Leader and Elite Four / Champion battles along with Monotype battles.
Gym Rematches were a lot of fun in HGSS / Emerald it's a good idea and i'm looking forward to seeing what you do with your custom region / leaders.
I've got a question about the type matchup's regarding the two new types you're planning on adding into the game, what are they strong against and what are they weak against? Sound seems like an interesting idea however it makes me think of a more Buffed version of normal type such as less types types resisting it. Cosmic on the other hand makes me wonder think it'll have several weaknesses due to it's foreign origin, i picture it being weak to Poison, Steel, Fairy, Fire, Ghost. and it resists Psychic, Ice, Dark and i'm not sure what else. so it'd be interesting to see just how the matchup's will work and how many pokemon are retyped to either or these.
Time travel has been seen briefly in Pokemon HGSS with the Celebi event (nothing else comes to mind) however in other fan games Pokemon Zeta/Omicron and Pokemon Insurgence have a really well done concept on this feature it adds endless possibilities, from a creative point of view you can add Classic / Nostalgic events such as a battle against Giovanni, Red and maybe other official characters or some of story related aspect from certain points where you have a side quest, a new area for Legendaries or even rare items / other rare pokemon such as Mega stones or fossil pokemon / other rare pokemon.
It sounds like it could turn out to be a really good game.
I'd like to know what kind of graphics you'll be using, personally i hate the Gen 5 trainer sprites where you actually see their legs, however some Gen 5 graphics are really nice they're smooth and shaded nicely, Though i've seen most games using them as they look washed out which isn't all that refreshing. So i just hope you're using colourful tiles either Gen 4 or 5 would be really nice.
Though the game itself sounds enjoyable so i guess i wouldn't mind what it looked liked as long as it's enjoyable to play.
I apologise if i gave criticised your game to much these are just personal opinions.
I also apologise if my message seems unclear in some way, it's pretty much all praise for the things you've planned thus far for your game so i'm really looking forward to seeing what you do with these features.
Best of luck in developing your game, I'm looking forward to being able to play it (:
