I prefer Zekrom to Reshiram mainly because I think that Zekrom has better aesthetics than Reshiram. Reshiram seems like it was a little too 'over-designed' which then made it seem akward and imposing. Zekrom, on the other hand, was quite a simple design which made it seem almost humble and not scream 'Hey, look at me! I'm a legendary Pokémon' (which Reshiram's design did scream, in my opinion).
As for battling strength, both have their strengths and weaknesses but in general they're both pretty strong powerhouses with some sexy unique moves.