I can't really pick an overall best one either. ME 1's overal main story was the best, but the sidequesting and exploring planets was mediocre and the inventory management was attrocious. "Before I sell this Regeneration VII, I need to check if any of my 6 party members still have a Regeneration VI. Oh, and I need to check the stats because this brand's Mark VIII pistol is actually better than this other brand's Mark IX."
ME 2 is almost the complete opposite, giving us only cramped, claustrophobic locations to explore, a main story that didn't pique my interest (It was only right at the end that I realize "Go look on the other side of the Omega Relay" wasn't the first part of the story, but the ultimate objective.) and a combat and character customization system that was too simplified. But it also had much better party members and side quests, and a gameplay wise the ending was great.
ME 3 probably would've been my favourite had it not been without the ending. As it is, it has the best gameplay, with finally a good balance between usability and customizability and, oh joy, an influence mechanic that didn't penalize players for not going all paragon or renegade, but with some baffeling choices in the story department: limiting player choices, way too much focus on Ceberus and, well, the part of the franchise that shall not be named.
So the best Mass Effect would be a remake the first game, with the party members of the second and the gameplay of the third (except with overheating guns. Fuck thermal clips.). Bioware, you know what to do!
(Okay actually, if they want to make it even better: Add some space combat already. And not just for the cool new gameplay. It'll make things easier on the writing department if they don't have to write a climactic final battle for the fate of the galaxy that the player can have an influence on. While I'm certain a better ending than ME3's would've been possible without playable space combat, I believe it would've been almost impossible to end up with something this bad with it. If they hadn't had to relegate the fight against the Reapers themselves to cutscenes, they wouldn't have had to contrive a resolution that could conveniently be accomplished by 1 or 3 pedestrians.)