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well, a problem with transparency is happening on ikemen plus ... see:
(...)
I would like to know if this has already been identified and corrected in the GO version

it's fixed for the screenpacks (to be more precise in old Ikemen Plus animSetColorKey was used incorrectly). As for the stages please upload the problematic one and I will check it out. Even if the problem is still there I know how to fix it (should be a matter of changing one of the bg.anim.mask lines in stages.go from 0 to -1 or maybe defaulting this value to -1).

It has been already requested to extend "1, 2, (...)" parameter feature to take into account additional parameters like music and stages, but this will require changes in the current code and the syntax will need to be different in order to parse such monstrosity. Probably in future, once it's supported,  syntax will look like this:

Code:

num={charname, stages/stagename.def, music=musicname}

using your example:

Code:

Ryu, stages/Suzaku2014.def, order=3, 1={Alex, stages/Shiyo/ring2014.def}, 2={Terry, stages/Shiyo/west2014.def}, 3={Sakura, stages/Shiyo/home2014.def}, 4={Ryo, stages/Shiyo/home2014.def}, 5={kfma4a}, 6={Kyo, stages/Shiyo/neogeoland2014.def}, 7={Sagat, stages/Shiyo/ayutaya2014.def}, 8={Ken, stages/Shiyo/wall2014.def},9={M.Bison, stages/Shiyo/drive2014.def}, 10={Akuma, stages/Shiyo/shrine2014.def}

[Characters] ; each character code can be contained in variables including the stages already ones
0 = randomselect
1 = homelessryu ,1 
2 = ken_speed_buster.def ,2,sound/rap.mp3 
3 = chunli/lee.def ,6,order = 2
4 = guillermo ,5,sound/vivaldi.ogg,order = 2
5 = cammyla.def ,7,order = 3
6 = mister_vegan ,3,order = 3
7 = agogouken.def ,3 , order = 4 ,hidden

[Stages] ;each stage on its own variable
0 = stages/training.def
1 = stages/road.def
2 = stages/bay.def
3 = stages/ruins.def
4 = stages/uglyplace.def
5 = stages/militarybase.def
6 = stages/chinatown.def
7 = stages/castle.def

[Routes] ; forced routes without taking into account the established orders
3 = 2,4,randomselect,1,6                      ;Chunli first vs ken, then vs guile, then some with order three, then vs ryu and lastly bison.
1 = randomselect,randomselect,randomselect,4  ;Ryu rute always be random fights from three first orders and lastly vs akuma.

[Status]  ;in char cns file
hidden.statedef = 666 ;overite the common one if exist for full games, or only has conditions if any has this char in hidden status for fun.

[Statedef 666] ;the statedef with conditions ,maybe lua is better for this
type = H

[state 666]
type= unlock
trigger1 = (if var (666) + (rank) = 999)     ;some amount of point for rank variable will unlock
trigger2 = ifselect(command = "QCF_z",2) ;some command in select screen will unlock

Unlockable Characters/Palettes/Stages - Supports Triggers for:
-Time Played
-Time Played Online
-Matches Played(can include online)
-Matches Won/Lost
-Arcade Mode results(Includes parameters for Characters used, characters fought, clear time, and times cleared)
(Fully Functional, unlocked data can be cleared through a branch I added to the Options menu~)

	gametime = 0,                --total amount of time played
	chars = {                    --[data related to individual characters]
		<charname> = {             --[subtable existing for each playable character in game]
			<modename> = {          --[subtable existing for each playable mode in game]
				--stats tracked after each match
				matches = 0,           --played matches count
				wins = 0,              --won matches count
				loose = 0,             --lost matches count
				draws = 0,             --draw matches count
				rankd = 0,             --total rank D count
				rankc = 0,             --total rank C count
				rankb = 0,             --total rank B count
				ranka = 0,             --total rank A count
				ranks = 0,             --total rank S count
				rankss = 0,             --total rank SS count
				--stats tracked after mode is cleared
				cleared = 0,           --mode cleared count
				consecutive = 0,       --maximum consecutive won matches count
				perfects = 0,          --maximum perfect matches count (flawless victory)
				continues = 99,        --minimum continuous count
				score = 0,             --maximum total score
				cleartime = 999999999, --minimum clear time (in ticks, so divide by 60)
				difficulty = 0,        --maximum difficulty level used to clear the mode
			},
		},
	},
	scores = {                    --[data related to global score rankings]
		<modename> = {              --[subtable existing for each mode in game]
			<num> = {                 --[subtable existing for each score saved - amount probably limited to 10]
				teammode = {0, 0}       --team mode selected for P1 and P2 side (0-single, 1-simul, 2-turns, 3-tag)
				team = {}               --slice containing character references (only 1 if single)
			},
		},
	},

 ; - hidden
 ;   IKEMEN feature: Set the paramvalue to hide a character:
 ;   1: cursor can move to this cell, face and face background are not
 ;      rendered (same result as hiding selectable characters in mugen by
 ;      placing them outside visible grid, but without need to create lots
 ;      of unnecessary select.def slots to do so),
 ;   2: cell can't be selected, art is not rendered (slot is ignored until
 ;      character is unlocked).
 ;   3: cell behaves like randomselect slot until character is unlocked.
 ;   Unlocking hidden characters is handled via [UnlockContent] section.

And Finally, Branching Arcade/Story Mode(Fully functional)

Is there a way to implement DirectX to Ikemen GO, just like the vanilla Ikemen?

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And about fight.def file, can you add a Bgdef for round, fight, k.o and win animations? This is possible using Add004 addon but impossible with mugen because you only have 1 simple layer for every action and it´s very limited to create good works.
Another thing that I don´t read nothing it´s about stages, please, can you add a 9000,1 portrait to them? With mugen you need to add a image for each letter or symbol but it´s very limited too.
I read that it´s possible use various portraits for select, versus and winner screens but, it´s possible do actions ( Interpolate Blend, Offset, Scale and Angle) with them?
Another thing that I like it very much in Add004 addon are the combo messages, it´s possible to add to Ikemen Go this feature?
Thank you very much for your work and waiting more news about it, see you and forgive my english...

Other than stage portrait, I'm afraid none of this stuff is currently on ikemen go plus roadmap. Join the project and start implementing them if you want to get these features in foreseeable future.

Quick question. Isn't there some limit on mugen where you can only have a certain amount of ports for stage select? What is the deal with that exactly? Not that I have 200 stages, but just curious if that issue would well still be an issue with this.

Also selfish of me to ask this one, but as someone who actually plans to use this, I want the animated ports(I've seen some others here also interested). We can all agree that we basically want it similar to say, older MVC series https://youtu.be/fNuX9cTkHJ4?t=31s animated, when selected they use "state 195"(whatever you have). I've seen it asked, but hasn't been answered.

Also hasn't been mentioned in a whileeee, but the announcer on character select, even a little note on how to do so would be appreciated.

Also, another thing, is there any possible way using this to integrate second round themes?