Comparing Varian to Thrall is kind of unfair- Thrall is the Horde's Jaina (even though she has less clout), and Varian is the Alliance's Basic Ca.. Garrosh (even though Varian has a few non-jackass moments), as it sounds like they're cementing in place for Cataclysm.

Now that that's out of the way, yes, Thrall's kind of a Mary-Sue. Not Rhonin-bad, but pretty bad, yeah. I think the reason most people love him anyways is because he's such a huge part of Warcraft, was created by Blizzard, can't do everything, and is more savior than full-blown god.
Compared with Rhonin: some pansy little mage created by an outside source who has done more than any character made in-house to change the course of history in Azeroth, save maybe Sargeras, and is the only reason several hardcore badasses are still alive/lived as long as they did. Also, he's married to Sylvanas' older sister and is the A'dal of Wrath- the insults never end.

In fact, even if Thrall was a little bit more perfect & had somehow managed to keep Grom alive, he'd still be better loved, because of both the in-house reason and because Grom is freaking legendary and is missed by all fans of badassedness.