There's definitely something to be said for just going the LCC route if you aren't a mid-to-high tier elite flier.

OP, how many total segments/miles would you say you'll fly per year? Is the travel primarily business or personal?

If you hold no elite status, your experience will be far superior on an airline that doesn't emphasize status to the degree that most alliance carriers do. Even if the non-alliance carrier *has* elite tiers (and most do), my experience has been that they don't punish the non-elites as harshly from a basic customer service perspective as the major alliance carriers do. This has been my experience flying non-alliance airlines in Europe, North America, and to a lesser extent Asia. It's more egalitarian...the gap in perks and treatment between the first-time flier and the top elite is much narrower than on, say, LH or UA. If I was in this camp, I'd pick the LCC every time - even if it was a mix of LCC's and I never really amassed much in the way of award power.

If you're a low-tier elite flier (a Star Alliance Silver level), then the service levels start to become more even. I'd probably lean towards the alliance carrier although I'd take a hard look at whether or not I'm paying higher airfares on most of my trips vs. a stable, reliable non-alliance competitor.

If you can reach Star Gold or higher, then the alliance route starts to look a lot better...although I'd still want to know what (if anything) I'm really paying for the privilege.