If you could replace or edit an existing mechanic...

Hmm, let's see... one thing I would immediately do is remove all overly-gimmicky evolutionary methods--such as turning your 3DS upside-down--and replace them with either level-up, trade, or stone evolution. Would most likely go with last one, since it's not that difficult when it comes to achieving; perfect middle-ground, if you ask me. Next, I'd introduce some type of Poké Ball that has much, much better capture rate than Ultra when using them on legendaries. This would reduce the need of spending so much money on regular Poké Balls significantly; only thing bad is that is might wind up devaluing Master Ball, but that should not be such a huge deal. They would still remain popular among people, since you're able to obtain only one throughout each game-play. Finally, I'd make it so that you're able to use certain moves in place of HMs. For example, instead of using Cut to get past small trees, you'd be able to utilize False Swipe, or perhaps even Slash. Instead of having to use Rock Smash to break small rocks, you would be able to use Mach Punch, Low Kick, or any other similar fighting-type attacks. This isn't my idea, though--somebody else had suggested it in some other thread--can't put my finger on who it was--but I personally like it. A lot, haha.
 
The option to save during a battle. I also agree with the user above about stupid evolutionary methods. I'd probably get rid of trade evolutions too though because it's just annoying for me. I'd also bring back the vs seeker and having a Pokemon follow you while you walk. Last thing I can think of is changing the encounter rate. I swear some of the games are so sensitive. I'll be trying to pass through a very small patch of grass and encounter three to four Pokemon on the way. I noticed this a lot in BW and it drove me so insane I had to use max repels constantly.
 
I came up with the idea of a character named Professor Palm who'd be the one to make the discovery that pokemon are "micro-evolving" constantly,
which over time may cause them to change in small, yet noticable ways.
For example, the stats incease that we saw for some pokemon, like Butterfree & Beedrill in X & Y & becoming able to learn moves
they couldn't before, like with Flareon & Flare Blitz.

In this idea of mine, the way pokemon evolve could change.

Some of the changes I have in mind is to have Eevee evolve into Leafeon using a Leaf Stone, Electabuzz & Magmar evolving into Electivire & Magmortar
by holding a Thunder Stone/Fire Stone while being traded & Rhydon evolving into Rhyperior by learning a certian move (I was thinking Protect, or a new rock-type
variant) then traded.

The purpose of this idea is to reduce data clutter in the games by removing pokemon-specific things, with the expection of Mega Stones & improtant held
items, like Grieous Orb.

EDITED IN:
Oh, & I was think Eevee could become Glaceon by leveling up while it's hailing or there could be a new evolution stone that I'd call
Glacier Stone.
 
I'd make HMs either replaceable like TMs or, like Endless suggested, remove them (and maybe keep Fly as a TM) and have certain moves work just like the HM moves/field moves would. There's no way in hell you'll get me to teach Cut or Strength to one of my main team members (unless it's for a challenge that prevents HM Slaves, of course), and I'm not too fond of replacing one of my team members with another just to get through an area. Additionally, I'd like for Challenge Mode to become a staple in the main games (really hoping it'll return in ORAS), and maybe even implement a "Lunatic Mode" for even more of a challenge. Said mode could have Trainers/Gym Leaders/Pokemon League members/etc. with more competitive-based AIs, making them have team setups and strategies that would be similar to what's found in places like the Battle Maison and Frontier. And, of course, the levels would be much higher.
 
I'd replace HMs with items or with Pokemon traits so it doesn't restrict a region to linearity to avoid the use of HMs. Then I'd make all evolutionary stones able to be purchased in a store since it makes no sense that some are rare and some aren't. I'd give rivals, E4, and lategame gym leaders full parties with semi-balanced teams that still fit with their type. I'd test out Fairy's immunity to Dragons and see if it was really necessary or if it was overkill, then I would add challenge and rematch settings to all games. I would also lower some Pokemon's evolution levels (like Noibat and Rufflet). I think that's it for now.
 
I'd probably agree with those who said change certain evolution methods, especially the trade-based ones. It's so annoying to me because I have no friends who play Pokemon in real life, I currently lack a second 3DS (so yeah can't trade in 6th Gen right now) and I also can't connect to wi-fi. There are so many good Pokemon that I want to use, but can't use because I can't do the required trade to evolve them.

Also, I'd make HMs be easily replaceable like TMs. That I mean, no requirement of a Move Deleter. And also one that may feel a bit weird, I'd get rid of routes with the very tall grass. I always feel like those kinds of grass patches are unnecessary, in 6th Gen you can now ride a bike through it which you couldn't do previously and I thought the purpose was to not let bicycles through it because well, it'd be too thick to ride a bicycle through.
 
What I'd do with HMs is to make it where the pokemon can forget how to use them in battle, but still can use them outside of battle,
Therefore putting the "Hidden" in Hidden Moves.

In this way, our pokemons can use all the moves we want them to in battle & still be able to use the nescessary moves, like Cut or Surf when they're needed outside of battle.

The move deleter would still has a purpose, as he can remove hidden moves so the pokemon can be traded.
(unless the game will only trade with the newest games, then it could be worked out where pokemon with hidden moves can be traded.)
 
Vs seeker brought back
Enough said....
 
Off the top of my head there are two things I would edit.
The GTS and player to player trading.

So the big problem with player to player trading is that there is no way to communicate with the other player when you aren't in contact with them over the internet or in person.
Obviously since this is a children's game you can't allow people to have a long drawn out conversation or cursing. But you really don't need much to communicate what you need.
There needs to be an emote button for 'yes,' 'no,' 'kinda,' and an option to propose exactly which Pokemon you want. When someone offers something it would be nice to say 'no' instead of just sitting there idling until they take a hint.

The GTS is flooded with people trying to trade less valuable Pokemon for more valuable ones, such as legendaries. This option should be available but the players should also be able to filter out other people requesting such ridiculous trades. Hopefully this would reduce the number people doing it, since they seem to do it for attention, and would make it easier to find trades people are actually interested in.
I'd also like to see the ability to search for trainers by what they are requesting. So let's say you want to trade an Abra but you don't care too much for what you get in return. You could search for people that are looking for Abra and then you can pick whomever has the better offer.
 
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