I'm glad you asked this question. At this point I'm debating whether I want to invest any money in the next set. My thoughts sort of echo what CaveTroll and doiron have said. When I first started I really enjoyed the boardplay element of the game and the struggle to balance between controlling territory and having creatures out. As time has gone on, the game has been getting less enjoyable. I think the biggest symptom of this for me is that I had more or less switched entirely to limited formats where this is less of an issue. MF domain destruction decks are a style I find relatively boring, which is why I have been regularly playing and posting about the Earthquake deck I have been using so that some of the key cards it is using that I think are too strong get weakened and I can get back to some more creature based tactical battles. As it is, when two MF decks meet is becomes a Magic style battle of who gets the key counterspell (negate, fissure) off at the right time first and much of the boardplay becomes irrelevant.

The glory gainer decks are even more so. I second the comparison to Magic, and if I wanted to play a game like Magic I would just go back to playing Magic. I don't think the gainers need to be removed entirely, just that they need to be essentially useless against good decks, except maybe for some marginal push you over the top cards like the ones in the first set (and even then, I'd be ok with a toning down of Caravan of Dreams).

One thing is I think people are playing these a bit more now since they are new and people are exploring what is possible. And I still don't think turtle decks are too strong. I need to play a good one more I suppose.
But here are are the changes I'm thinking to make alternate win decks less prevalent:
Evangelist: some other ability that doesn't give glory.
Aurora: just dropping for now
Cathedral of Xosa: 4TTX
Hunting grounds: only spawns if there are less than 2 mastodons.
Caravan: can't be the target of spells or abilities (so rift + caravan will no longer work)

Like I said I need to play some turtle decks more to decide about:
Mana dome, shield generator, peaceful oasis

What about Benefits of Wisdom, Benefits of Numbers? Are these fine?

Any card I missed that makes the game less fun/interesting?

Personally I like the ability to gain glory from ways other than flux wells. The problem arises when flux wells is not the preferred method of gaining glory. Borderlands brings about a lot of alternate ways to gain glory, and several ways that punish players for seeking glory the traditional way (Aurora, Hall of Justice). What Borderlands doesn't bring is any additional incentive to capture flux wells. I think a large part of this problem can be mitigated by changing/adding cards.

Off the top of my head here are some cards that could encourage capturing flux wells:
-An enchantment that allows only the player with the most flux wells to gain glory.
-A creature similar to Royal Guard that gets bigger for every flux well you control.
-A "flux caterpillar" creature that morphs into a "flux butterfly" creature when you control 3 or more flux wells.
-A spell that lets you draw a card for each flux well you control.
-An enchantment that gives each creature +1 Attack for each flux well it's controller controls.
-Etc., etc.

If alternate ways to gain glory exist in the game, then there simply have to be cards that reward a player for gaining flux wells to keep the opportunity cost somewhat balanced.

More cards that cause opponents to lose glory could be useful (although that does have the risk of making games last too long.)

Since a lot of these glory-gaining cards are enchantments, another reason these strategies are strong is the lack of enchantment removal. Yes, there's Mystic Feedback, but at 3 domain, it's not always a feasible choice. I propose the idea that Disenchant becomes an unaligned spell while MF gain Mystic Feedback (it could probably be dropped to 2 domain then). Unlike creatures and buildings, enchantments (usually) have to be targeted by a spell to remove them; they can't be attacked by creatures. Disenchant doesn't really pull off a unique feel, unlike Lysis, as variations of enchantment removal are going to be much more alike than variations of creature/building removal.

I think that alternative methods that make you engage your opponent are a good idea.

I think that ideas like my deck can be a little boring. I only constructed it because I wanted to win, obviously.

Vortex for example is cool. Putting something in the middle of the map certainly forces action.

Other cards that give glory for interacting are fun as well. People's Champion for one.

Maybe a card that gives glory any time you destroy something belonging to the enemy.

Etc.

I'm fine with alternative way to win...
with one restriction!
The game must have must have many different ways that seems equally good to win.

This is just to remind you what, in mathematical sense, makes games including chess and Go draw in the brilliant minds.

I echo them.
Flux well dominance should be THE primary and most often strategy.

The problem with the glory generating tatic is that they are consistent and less reliant on uncontrollable things like terrain, where the enemy is etc. Its a good thing, but now what it should be.

Now, im suggesting a way to partially solve this. Some of you may remember somone asking about having higher variations of flux cost, to which i suggested doubling all flux income and costs as to be able to have a higher variation of costs. (like if now something costs 2 flux, when doubled it cost 4 flux. and we can have something cost 5 flux, or 2.5 flux in the old method which is not possible)

Double the glory to win, and double flux well domination glory gains. Tweak the glorly gaining cards(some may need to be buffed!) but overall, it takes LONGER for said cards to win, giving a better chance for the other non-turteling player to win.