I confess I've never understood the 'clunky' combat comments about the first game.
The cover system is easy to use, you shoot from cover just like the following games, the lack of a global cooldown means you have far more options available during combat.
What occurs to me is that it must be down to how the dice roll requires you to level up your skill with the guns. Bioware hid the dice roll behind faux real time combat but while that worked for Dragon Age II on the consoles, the shooter veneer of Mass Effect had people expecting shooter combat.
Perhaps it was my mindset going in of expecting more of a classic Bioware combat system that made me like the one in Mass Effect so much.