Nintendo developed Zero Mission just a few years ago, and that game actually encouraged sequence-breaking, just like Super.
that's why those two are my favorites. in that order.
and it's already been discussed what can no longer be done in Prime 1 and 2, because people at metroid2002.com have imported them and studied them.
there is a way to get Space Jump earlier than intended in Prime 1, but as of yet you can't get it first. which means you actually have to fight Hive Mecha again, which sucks. most of the PAL changes are present in Prime 1 as well. despite all that, the game is still pretty breakable. but oddly, the narration present in the PAL version ain't in Trilogy, which baffles me.
Prime 2 took a bigger hit. bomb space jumping has been taken out of that game, making a million tricks undoable. considering how few sequence breaks were in Prime 2 at the get go, Prime 2 is almost unbreakable now. it's comparable to how Prime 3 is.
i wonder if any changes were made to Prime 3...
i just entered Magmoor Caverns in Prime 1, and saved before the Dark Alpha Splinter in Prime 2. i'm enjoying myself with both games so far. i still love the Wii controls, especially the Jumpball.