Ash - I'm with you on that one. I think when it comes to movies, script and direction play a HUGE role in the chemistry that two actors share. That's why the same two actors appear to have great chemistry in one film and almost none in another. There are some exceptions of course, like SRK-Kajol who have sizzling chemistry regardless of the script. However, for the majority of the actors it's most often the script/direction that provides the spark they share on screen.
Anu - I don't think Jai-Meera would've been any better if other actors played them. The flaw lay in their characters and the storyline. Take KANK for instance - SRK and Rani have a decent amount of chemistry together in general. In that godforsaken movie though, I saw absolutely NO chemistry at all. Why? Because Dev and Maya sucked big time. Priyanka and Harman wouldn't look half as bad together in a well directed movie as they did in Love Story 2050.