In no particular order: the early-game shooting mechanics that make you wonder how Shepard ever got out of basic training, the ludicrously overpowered biotics that, once leveled up, can basically be rotated to permastun enemies, the Mako driving controls and physics, RNG equipment upgrades that make it difficult to get meaningful late-game armor upgrades without save scumming, the fact that every indoor environment outside the main hubs uses one of three maps with different props all come immediately to mind.

Note that the Legendary Edition addressed a couple of these, specificially the shooter mechanics and Mako controls.

With that said, ME1 is one of my favorite games of all time, warts and all, and despite the fact that I didn't get into the series until after Andromeda released, it's probably one of my most-played, as well, with at least one 100% Insanity run on every character class (with at least one per class carried through ME2 and ME3).