Well I think much of the praise directed at him is because he ended slavery and I don't think he deserves as much credit for that as he gets.
As for preserving the union, yeah, he did well, but wouldn't that have been expected of almost any president in that situation? I don't mean that they'd be expected to do as good of a job, but they'd be expected to fight to preserve the nation, and the North had pretty significant advantages that should have resulted in victory under any decent leader.
Reasonable arguments can also be made that, considering Lincoln's motives weren't based on slavery and he would have kept slavery if it preserved the nation, that all the lives lost weren't worth keeping the South. Then end result was of course great, though.
All in all, like how we measure presidents in general, Lincoln is judged in large part due to the circumstances and opportunity of the time. He certainly did well with those circumstances and opportunities, but he didn't do much to create them.
One of the things we often forget with the benefit of hindsight is how weak overall the leadership of the nation was in the years leading up to the war, and from the very top down. There hadn't been a two-term president in approaching four decades, since Andrew Jackson, and pretty much the entire bunch in between make up the lower reaches of "top president" lists. So while we might expect a president to lead the country through that kind of crisis, just on that measure alone it is a completely different time.
That doesn't even take into account how fragmented and state-centric (not even region-centric) the nation was back then.
I tend to think that Lincoln saw slavery, regardless of his personal feelings on the institution or race, as not only the single overriding cause of the Southern rebellion and the attempted split, but something that if not eliminated entirely as soon as possible would rise again as a national problem. Or as an international one, with Britain and France and most other European nations either having a passively negative view of the institution's continued existence in America or actively pressuring for its end. He could see the problems arising within his own party over the issue, mostly among the radicals who wanted a complete stop to slavery immediately (and harsh treatment for the South).
No matter what, slavery would have ended in America soon enough; in an industrial world even basing agriculture on that system didn't make much sense economically. However, it really came down to ripping the Band-Aid off all at once or pulling it off gradually.
Of course, thanks to John Wilkes Booth, in the end the South had the Band-Aid ripped off at knife-point, and weren't too appreciative of that.
