I consider every single flagship Pokemon game to be a strict improvement over its predecessors in terms of mechanical improvements (although some games are better than others as a complete package, like Gold/Silver and Diamond/Pearl).
Gold/Silver: Massive improvement over gen 1. Added dark and steel types which balanced out the game (psychics were OP), split special stat into Special Attack and Special Defense, breeding, held items and weather effects to name a few.
Ruby/Sapphire: While omitting several pokemon harmed the game, the addition of natures and abilities did wonders to give previously similar pokemon unique flavours. Also double battles, which rocked.
Diamond/Pearl: Attacks made physical/special on a move-by-move basis, as opposed to being type-based. This was HUGE and the most important improvement in Pokemon history imo. It made so many older pokemon more viable, and opened up loads more strategies. Also Cynthia was the coolest of the champions and one of the toughest.
Black/White: Addition of hidden abilities, and new battle types. Probably the game which innovated the least, though it made up for it by adding a ton of new Pokemon, having a genuinely interesting story and villains, and really fleshed-out and challenging endgame content.
X/Y: Mega Evolutions. While at first glance Megas seem like a gimmick, they can mean a lot for the game and open up a lot of strategy on a competitive level. Since items are so important to top end strategies (Choice items etc), the mega evolutions in many cases feel don't feel like a strict improvement on said pokemon, but rather an alternate way of utilising them competitively. With the addition fairy types to counter the overused dragon type, small stat buffs to several older pokemon to make them a bit more viable, and a very robust and easy-to-access online multiplayer, this game felt like a love letter to the more competitive players more than anything. The Mega Evolutions were just a way of doing this in a way that could be marketed at the child demographic. Clever Nintendo, appealing to both their core fanbases at once with that.