Pretty much. Once you catch a stronger version, no point in leveling up the weaker pokemon. I've reached the point where there's no reason for me to level up a pokemon whose base attack power is 60 (maybe 70 as well, depending on skill) or lower.
Lame, I've been leveling Squirtle like crazy hoping to get to Blastoise. Oh well.
Oh and also for the other question, can mega evolved Pokemon only be matched 1 row at a time?