having also shot both, for fishing, the d5000 is my pick. and as gimicky as this may sound, a lot of it revolves around the flip down lcd screen. ever tried to get a good low to the water shot while looking through the viewfinder? good luck. guesswork at best. while im sure there will be room for improvement with the ability to focus through the "live view" lcd screen (although you get to choose anywhere to focus on via a "focus box" you can move around with the directional button, its nowhere near as fast to autofocus as the 11 points you have while looking through the viewfinder). there is a way around this, though, that while it may seem a bit odd to have to do, no other dslr offers both this feature and the sensor (the same as the more expensive d90) that the d5000 has. yet.
couple this feature with the incredible 10-24 3.5-4.5 wide angle zoom (http://www.kenrockwell.com/nikon/10-24mm.htm
) that nikon offers, and youve got from what i believe to be the best combination of photo quality, lens options and fishing friendly features, all combined in a lightweight package that wont bog you down (as much) while fishing all day.
one big thing that ive found that keeps people from packing this expensive investment with them is the right pack. heres what i use-
seems like a pain in the ass, but whats the point of buying a nice camera if its never there for you to use because you "didnt want to pack it in, or plan on running back to the car when you need it". yeah right. its worth carrying with you, and that waterproof ROLLTOP has yet to fail me through both downpour and shine. the zip top version is NOT waterproof, so watch out.
ive got a buddy with a T1i and another with a T2i, both love 'em. no complaints, just a pain to get the shots an inch off the water. been there myself too. maybe its just my fetish for low angles...they just catch my eye better. be glad to try to answer any other questions you might have- hope this helps.