A show reaching syndication (88 episodes) means it can re-air on other smaller networks. Producers and actors of such shows will get money even if the shows are no longer produced, as long as it airs somewhere. Shows without syndication (less than 88 episodes) will only get revenue from DVDs. That's why TV studios always push for their shows to get to the 88-episode mark, even if they have to produce at a loss (unless they only have 40 episodes and are losing money, then they'll let it die).
Gotham already has 88 episodes after season 4, so WB doesn't really have any incentive to push it past season 4, but 100 is considered a better number for syndication deal (i.e. selling to other networks) so maybe WB will order a half-season so Gotham can get enough 100 episodes.
I believe the most well-known Tom Welling-related problem of Smallville is he refusing to wear the Superman suit (or not portraying the "real" Superman).