I think it sucks, but at the same time, it's like thinking your political leaders suck. It's kind of useless to have an opinion on something you have no voice in.
That said, even though I know my angst over forgetting half of what's going on while waiting for a second cour is pointless, and that it'd be far more mature to just let that go and angst over things that actually matter, I...go ahead and angst anyways.
I guess first world problems are my prerogative for being born into the life I was.
Furthermore, while you've given two examples, they're also about the only examples I can think of (don't really count shows like...oh...Gintama...or Natsume...for instance). So, I'm not sure I'd go so far as to say it's a prevalent issue. Yet.
In some ways, super fast subs are kind of a bad thing. In the old days, since subs were so slow, I'd just wait 'till a show was completely subbed (and often, the subs weren't available anyways, until well after a show had ended), then watch it all in one go, without feeling like I was depriving myself of entertainment. In that case, splitting up a season had no practical effect on me.
These days, with same-day subs for so many shows, it's hard to take that approach, and thus any delay in continuing the show is agonizing. For me, at least.
I can barely stand waiting one week. A whole season, for a show that had real momentum, is painful.
As to your two examples, the split wasn't as bad as I thought it would be for Zero. There was a noticeable shift in direction and momentum between the first season and the second, and to be quite blunt, the first season was actually really dragging, as much as I enjoyed it. Now, if they had split the second season in half with some long period of time, I'd have really been pissed, as there was real momentum going there. As for flowers and girls and strange looking mech, I didn't enjoy it, so I have no real valid opinion on the merits-or lack-of splitting its season.