Favorite Metroidvania is a difficult choice, there's like four games that immediately come to mind. Metroid Prime, Metroid Zero Mission, Dark Souls, and Guacamelee all stick out. I guess by default I'd have to say Metroid Prime because I think it's an almost perfect game. The backtracking in the endgame artifact hunt is probably the worst part, but on subsequent playthroughs you can collect them a bit more normally because you know where they are and how to find them. It just has an amazing sense of exploration and Tallon IV just feels so fleshed out and organic. The soundtrack is really excellent and atmospheric and it adds a lot to the feeling of being on this alien planet (though admittedly my favorite song is the menu theme, which isn't really an atmospheric thing at all, but I just love how it sounds and it reflects the vibe of the game very well regardless). A plus side is that I love so many of the boss fights, in particular Meta Ridley. Thardus and the Omega Pirate are some other particular standouts, and I appreciate how some of the encounters (Flaahgra comes to mind) are more of a puzzle than a boss fight.
I also wanna talk about Guacamelee a bit, just because it's probably my favorite 2D Metroidvania. I think where it most stands out is its combat system, this sort of beat-em-up/fighting game style where you just have a ton of options and combos that you can pull off as you fight hordes of enemies. It doesn't have quite the same sense of exploration as most Metroidvania games, but the levels are still very well designed and the fighting is a ton of fun. I haven't gotten around to trying out Super Turbo Championship Edition, unfortunately... I've been meaning to, someday I'll get around to it. It also has some exceptional boss fights, and the dimension swapping mechanic is really one of its best features that adds a lot of creative ideas to the level design.
As for favorite transformation in a game... for some reason I always really liked the car in Yoshi's Island. I don't really know why, it's probably just a nostalgia thing honestly. When I first found it as a kid I just really enjoyed the sense of speed I had while racing through the level (I don't think it's even the fastest thing in the game, I think the helicopter and super baby Mario are faster). I dunno, something about it just felt satisfying to me, I liked all of the transformations in Yoshi's Island but the car just especially clicked for me.
Some other transformations that I have fond memories of... UFO Kirby in Kirby's Adventure/Nightmare in Dreamland. Nowadays UFO Kirby isn't especially interesting because every power has a ton of features, but in the context of Adventure, UFO was the most radical ability Kirby had ever had access to. Super rare, four different attacks, permanent flight... the norm for Kirby at the time was that abilities would have maybe two different functions if you're lucky. UFO was just super versatile and it felt like a real reward to find and eat a UFO enemy or to luck out and get it through a mix.
Also, this is a bit of a stretch in terms of "transformation", but I liked the segment in Metal Gear Rising where you hacked into and took control of a dwarf gekko. It was a funny change of pace and the animations for the little guy were pretty charming.