Hmm no replies yet? A pity, this does look like a decent farmer, or could become better.
Firstly, going to supply you a link to an old FG farmer that is somewhat similar to yours
http://elementscommunity.org/forum/index.php/topic,1615.0.htmlI used to play a mostly upgraded variant of this and It did good enough until I moved onto a CCYB variant.
Secondly, Though I haven't tested it, there are several problems here with your deck.
-You are using FAR too much aether quanta with a deck that doesn't reliably produce it.
-You are failing to use a very good shield to take advantage of flooding (Bone wall)
-You could be putting those skeletons generated from boneyard to better use.
I think your deck could use the following.
-A fallen Druid
This will help against several false gods. It may help in making akebono slightly more beatable, while converting your skele's into far better creatures, or turning things such as pufferfish into safe to eat creatures for your otyugh.
-Bonewall
This should be obvious. Against incarnate and neptune, this shield is capable of reaching some ridiculous numbers, while a very good defense against many other FG's.
Maybe try this to start with.
-1 momentum: You won't need this. If a shield is blocking you, just use eternity to rewind your own creatures until you can overcome it.
-1 Quint: Too many. Some creatures you won't need to quint. generally 2 quinted creatures, depending on the match will see you through.
-4 supernova: This might be a personal preference here. I'm not so sure how useful they are to you. In this sort of deck I'd use Quantum towers, but I can see some advantage to it, so up to you if you change them for quantum towers.
-4 Phase shield: Just too much aether usage.
-1 Miracle: You should have otherways to regenerate your health, as long term options.
-1 Electrum Hourglass: Too many for a 40 card build.
+4 sundial: Uses up light quanta, good use of time quanta. More temporary stall than dimensional shield, but also helps get through your deck quicker.
+4 quantum tower: Pillars will do if you can't replace them with the upgraded tower, for now.
+1 Fallen druid: Make some outrageous mutants. Also may help PC if you get a mutant with steal/destroy
+1 Elite Otyugh: Eating things as soon as possible is very important vs most gods.
+1 Bonewall: Enjoy a never ending supply of bones to protect you.
+1 Feral Bond: More healing
I think this should do for a start. It's a lot more similar to the FG farmer I linked you too, and will probably require some adjustment in order to play, but I feel the changes will help while also keeping your original idea. In order to stay alive though, you'll have to take much more damage at the start before trying to chain sundials or use those dimensional shields (This will vary between the FG's, as some with large weapons will require the chain of sundials to start earlier) (Save the bonewall for as long as possible). The only other thing is that with bonewall and flooding, timing of playing both will be pretty crucial.
One other thing to note: If you do use the druid, keep in mind any FG with Twin universe will take advantage of larger mutants made, which can backfire very badly depending on the element of the mutant.
Upgrades: Agreed that you should upgrade the phase shields. Towers next maybe.
Hope this helps.