Tom Scocca at Slate, who shares my antipathy for the baseball wild card for most of the same reasons (as well as a couple I had not thought of), argues that the new proposal to add a second wild card actually turns out to be a good second-best option (the best option being eliminating the wild card altogether, which, unfortunately, is not going to happen).
As Scocca explains, the already-overstuffed schedule, along with MLB's recognition that things cannot go any deeper into November or earlier into March, means that the addition "wild-card round" must be short--one game or at most two-out-of-three. Weird things can happen in a short series. So this creates a meaningful incentive--currently missing--for a top team to win the division rather than settling for the wild card--avoid that short series. It also means that the two best second-place teams go head-to-head, rather than "battling" one another by proxy against very different (particularly in difficulty) schedules.
True, it also may mean more 87-win teams in the playoff race every year. But again, this is just a second-best option.