Well--I haven't done any "public" recs (as in, posted to a community and aimed at everyone in the community. I have made recs in, say, a public entry in someone's journal/my own journal, or comments on a public entry in a community) but when I rec things one-on-one, I tend to mention what I think are the flaws. I might say something like, "Author X is a little too fond of deus ex machina endings, but his worldbuilding is fantastic and his writing is engaging". I do this for a couple of reasons... first, I feel like knowing about the flaws beforehand can make it easier to look past them (if I know beforehand that something has a lame ending, I get less invested in the plot and focus more on other aspects, so the lame ending doesn't really upset me when it happens). Sometimes, something's more enjoyable if it's in line with my general expectations. If I'm looking for something serious and I get cheesy fun, I'm going to be a little put out, even if the cheesy fun is something that I might normally enjoy. Second, it seems like it's only fair to warn the person ahead of time, just in case that flaw is something they really hate. Sort of like warning for potential squicks. I mean, the point isn't to get them to read it no matter what--the point is to tell them about something I think they might like.

I won't go into the flaws in too much detail, or dwell on them much, though, if I liked the story. I just try to mention them in passing to give the person a better idea of what to expect.

ETA: Oh, and if the flaws are something minor that I think might be easily overlooked, I might not say what they are specifically... just something along the lines of, "It has some issues with grammar, but overall..." or "It has a few problems/issues, but I think they're relatively minor."