I'm not going to lie, I lean more toward EVGA. Until you've owned one you just don't know any better. I've owned both, card prior to this was an MSI AMD 6870 Twin Frozr II.
However, there is a difference between them.
If your going to SLI
the air flow out the back bracket of the tower is better than on top of each other and going into your case from the non-reference cooling. You'll have hotter top card with MSI even with the TF2 over EVGA's top card. Your top and primary card takes the heat dissipation coming off the bottom card along with it's own heat as heat rises in side your case.
Now if your only going with a single card then it's heat dissipation is no problem in a well ventilated case on a single MSI TF2 card and will actually be cooler than the reference design.
If you plan on changing your still functional cards within 3 years than the EVGA warranty wont' matter. If you keep them until they die then most likely that series won't be in production any longer and you end up with a current model of same performance upgrade.
Both companies make good cards, so you can't really go wrong choosing either. It's really just preference. EVGA is exclusive to Nvidia. Great forums
and support as well.
Here is the image of my card with a high flow bracket and back plate. The high flow bracket does lower temp by 1-3%C by lessening air restriction out the back flow bracket.
The back plate is purely vanity and minor protection. Sure does bring the card together nicely.
Good luck in what ever you choose.