The single biggest problem with MKR2 is its length at 29 episodes. The first season (spoiler free link) was slightly bloated at 20 but had the advantage of the changing tone as Cephiro started to crumble. Season 2 on the other hand needs to be cut, preferably with a chainsaw, down to about 13 episodes.
The best thing about the second season is that it does fix most of the problems with the first season.
In particular it directly addresses the post-traumatic stress induced in the young ladies by having to kill Princess Emeraude . In essence the girls are not handling things well back on Earth, meet up again at Tokyo Tower , and are promptly summoned back to what's left of Cephiro .
In the absence of a Pillar three other countries  are sending invasion forces to become the pillar and shape Cephiro to their liking. Meanwhile the surviving fighters and mages are trying to hold the pieces together until a new Pillar is born and rebuilds Cephiro.
Hikaru also acquires an evil twin, Nova, who was created out of her guilt and self hatred when she killed Princess Emeraude. Nova is quite well handled throughout the series, particularly with her being able to shatter Hikaru's sword at one point. The reclamation of herself, and the consequential reforging of the sword, is also well handled .
Reconciling Cephiro with the other three countries is ultimately achieved by the Magic Knights, one per country, and Fuu's episodes with Fahren are the best of these.
I also have to revise my opinions of Clef upwards again. I was deliberately watching this time around with a very critical view of Clef, and the evidence to support it just wasn't there. It is still true that he should have done more to warn the girls during the first season, but he holds nothing back in this season. Indeed he basically gives Hikaru the information needed to achieve the right ending.
Which, naturally, is for Hikaru to abolish the Pillar system when she becomes the Pillar. The new Cephiro will still be a world of will, but all of the people of Cephiro will share responsibility for building that world.
One nice touch is that the two opening credits  are mirror images. The first opening starts off with a beautiful Cephiro and ends with the ruined version, the second opening ends with a view of a beautiful Cephiro. 
However Uni and Fuu should also have had to deal with evil twins. The fact that they didn't somehow lessens Umi and Fuu as characters; it implies that they didn't suffer as much from having to kill Princess Emeraude. I would also have preferred to see the Magic Knights become the Pillar jointly, and abolish it together.
As it is the second season is massively unbalanced, and the episodes with Umi and Fuu are mostly filler  to distract you from realising that they are supporting characters. An angsty romance is introduced for Hikaru , and a romantic triangle is introduced for Umi to further pad out the episodes .
Magic Knight Rayearth is still a very pretty series to watch, and I do enjoy it, but it is deeply flawed.
 Yes, I did just fit David Weber and CLAMP into the same sentence. Your brain may now melt.
 And that would be the link with spoilers.
 I think they should have met at a nice cafe somewhere far, far, away from Tokyo Tower but that's just me being Genre Savvy.
 Not much. There's a castle. And some wastelands. That's about it.
 Whilst they are called countries in the series, worlds is a better word. All three require spaceships (or equivalent) to get to Cephiro and the shapes are definitely world like. Ish.
 If overly long. But that's true about most aspects of this season.
 On the US DVD release. I'm aware that there was a third opening but I don't think it was used in the commercial releases.
 The second opening is also a very pretty song, but was actually improved by the translation. It is the only time in my experience where a translation has been better.
 Occasionally very sweet filler sometimes, but still filler.
 With Lantis, the younger brother of Zagato. Yes, the Zagato that Hikaru killed. Nova has fun with that when it develops.
 Clef and Ascot? And Umi picks Clef? Really? I don't know how active MKR is in fanfic circles but I suspect that the shippers had a field day with that one...