have you played with both phones in the store...checked them out? done some tasks you would normally do?
its all preference.
i have the thunderbolt, it is fast, smooth, has pretty good battery life (i go 12 hrs easily with what i would consider heavy data usage and light phone usage)
has great signal strength ect. i really cannot complain about this phone.
the battery was a big complaint for most, but OEM batteries can be bought for about $10 now....buy one and swap it in when needed.
when i played with my buddies D3 i was seriously disappointed. Blur really kills the phone. felt sluggish changing screens (even without live wallpaper) slow to open up apps (slower than my TB at stock speeds) signal was just about even, data speeds....duh.
screen on the D3 is terrible IMO. everything looks washed out BIG time next to my TB. even though the D3 has the resolution advantage, it looks like crap IMO b/c of the screen technology (search pentile matrix) greens were especially bad (very pixelated looking) anything that wasn't vertical or horizontal was kinda jagged, fast moving objects had a shadowing effect...just a bad decision by moto to use that screen. the hardware is very nice though. i LOVE the look and feel of the phone. very solid, love the keyboard and would probably use it if i wasn't completely satisfied with virtual keyboards now.
all in all, its a decent phone. i would still take my original Droid X over the D3 or DX2 any day...not sure what it was, but the DX feels faster than both, and you dont have to deal with that terrible screen. but the Thunderbolt is leaps and bounds above any other phone on verizon right now....thats just IMO