I think that 5-10% of the time, card draw can really hose you. I was playing a game the other night where I constantly had a handful of recons, and that just didn't do much for me. I'd say that's the exception though, not the rule.
However I have to totally disagree with your assessment of balance. The scenarios are quite unbalanced. Like Matt I don't have a problem with this because, as he said, you just play the scenario twice. My wife and I have consistently done that as we've moved through 30+ games. However if you look at the results at
www.memoir44.com, it's obvious that there is a significant imbalance in many scenarios.
Pegasus Bridge, for example, is 491:197. Even more notably Omaha Beach is 48:239. The newer scenarios from the expansions don't have enough plays yet to be significant, but two that I found particularly imbalanced were Knightsbridge (6:18) and Breakout at Klin (1:10).