I'm in the camp of loving Frontier, but still wishing some things were better. Even there though, I have to admit that it's not like the earlier TV series were much better on most of my criticisms, and sometimes worse.
1. Inconsistent animation: This one struck me a lot: shifting models, strange viewing angles, the occasional motion that just looked like spastic flailing around. Partly this came out of different studios being used, and it's not like this wasn't striking in SDFM. Still, I could have hoped for better.
2. Pacing: Some episodes, even with valuable character development, felt like filler, and others felt simply rushed. The ending certainly could have used more time. On the other hand, the climactic battles for all three have been really plowed through, and this was the shortest series of the three and never really went more than an episode without things rolling along. By contrast, 7 spent the first third of its run not really developing both plot and characters at glacial speeds before things really started happening, and the last episode was as muddled and rushed as anything.
3. The triangle's end: At first I was dissatisfied: it seemed like a kludge at best, another trick played on the audience at worst. But the more I consider it, the more it makes sense to me, wheras I still find Macross 7's resolution to be dissatisfying on that front.
4. Sexin' up: I can't really complain on some level of sex/innuendo/cheesecake/etc. It's not like it's new to the genre or the franchise: even on TV, SDFM had its share though it was milder stuff to suit its era, and 7 had less but was aimed for the youngest audience of the three. I do wish that it had been less of a lolicon slant: it's not as extreme as some things, and I know much of this has been done to death, but it's striking. Mylene was young, but I think it's telling that Mylene was 14 and cast in a movie as a 16 year old, and Ranka was 16 and cast in a movie as an 11 year old. And that's to say nothing of Klan: I feel the focus on her enormous-breasted giantess/loudmouthed little loli elements distracted from exploring her other dichotomy of a Zentraedi that's proud of being born into human culture, yet also of her traditional role as soldier. I could have done with several fewer suggestive shots at dramatic moments, for that matter, like so pointedly focusing on the T&A angles when Klan did her EVA-style launch in Island 1. Still, this was stuff I could live with: early in the show I feared it might collapse into another sexed up fanservice show, but the trend fortunately did not build further.
5. Hero mechs: One thing that impressed me greatly in SDFM was having the aces and the grunts go out there in the same plane, with minor differences like head design and paint job being there mostly just to show who the heroes are: if someone did better, it was from being a better pilot alone. Of course, every installment in the franchise since has focused very much on aces keeping to advanced prototypes and upgunned custom models, so this isn't a flaw of Frontier. If anything, this dialed it down a bit by putting out a whole squadron of VF-25s complete with cannon fodder models, putting the two really customized models in the hands of junior pilots and used for more support than front line fighting, and making the VF-27 a primarily antagonistic fighter.
6. Villainy: You mean the giant space bugs are our friends? It was a gradual build showing that there was more shady stuff happening on Frontier than Vajra attacks, even if the pacing of it seemed sometimes jagged. A lot of people got that the Vajra weren't the true enemy as the series progressed, but making them not necessarily an enemy at all felt very rushed for many/most, compared to the speed at which it was shown that the Zentraedi and Protodeviln weren't necessarily evil or impossible to make peace with in theory. Still, for once the aliens were actually alien, and it followed up from the late lesson of SDFM that the real danger isn't just more Zentraedi fleets and Protoculture remnants, but rather the warlike and controlling natures within humans and Zentraedi alike. And I was pleasantly pleased to see a major, and vicious, villain who didn't telegraph it on her first appearance.