You've already seen the biggest disadvantage to inverted mounting, it makes starting harder. Inverted engines also don't always idle as well, and the idle mixture setting is more critical. This is all caused by what Minn said, excess fuel and oil pooling in the plug.

To get an easier to set, and slower idle with an inverted engine, some guys go with an onboard glow lighter. But I've seen guys at my field run inverted 4-strokes with no on-board glow, and absolutly no problems at all, nice idle and everything. And I've seen guys never manage to get an inverted engine to run right. So, YMMV. In general I think it's a little harder to get everthing just right on an inverted engine, but once you get it right, you shouldn't have any problems.

I personally find side mounting, with the muffler down, is the all around easiest way to run an engine. If I ever get around to designing a trainer, that's how I'll mount the engine. (It's harder to flood, since the excess fuel will pour out of the muffler, though you can still flood the crankcase).