Well, there is a much wider range of DLC for Rock Band 2 (not everyone has wi-fi and/or wants DLC), and RB2 for Wii has all the features of 360 and PS3 versions, whereas GHWT for Wii only allows online play between two Wii consoles over Wi-fi.
When comparing graphics, GHWT for Wii has graphics that are sub-par compared to WT for 360 and PS3 (as did GH3).
On a personal note, I prefer Rock Band 2 mainly because the setlist, in my opinion, is better and because the in-game characters look more realistic to me.
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