I just recently bought my HARP books and haven't actually run a game (and may never -- but for reasons unrelated to HARP itself . . . ), but I know what you're saying. That's how I felt about MERP, which I did play years ago. As a player, I loved all the character generation detail, but I tended to gloss over some of the game mechanics as a GM. For example, I didn't pay much attention to activity percentages during combat rounds, and tended to use common sense for how much a character could do in any given round.
Of course, the reason I bought HARP is that it looks like it has the detail I liked about MERP but rules closer to how I simplified MERP. So, as I learn the game, and make note of which optional rules to use or not, and what house rules I might impliment, I find I'm not thinking about simplifying it much.