The current iOS Special Ops is severely broken. Vision, whether a team-up or enemy boss, is always invisible except when you hit him or when he attacks. Omega Sentinel's Change Protocol power allows her to go from scrapper to bruiser, but then she's stuck as a bruiser. Ultron Prime is missing from the Spec Ops Mission 3 boss battle.
However, good progress can still be made in spite of the problems. I would have to say that I haven't really lost any time working my way through the task list. Here's how I played it so far:
Tasks 1-6 and Omega Task 1-3
Started off with runs through Spec Ops Mission 1. Knowing that I need Exoskeletal Battletanks for Task 4, I did only easy and medium fights to complete Task 1. This lowered my mission score, but allowed me to finish all the tasks up to and including the first research as well as the first 3 lockbox tasks. I completed the 2nd lockbox task outside of Special Ops. So far so good. Mission 1 is 3-starred and still had something like 300 U-Iso left.
Spawned a Group Boss and started working on Mission 2 making sure to do each mini-boss fight separately to make sure I got credit for Task 8, but left X-Ray boss hanging around for after my next research in order to complete Task 13. Thankfully, we have this Wiki available to us, because knowing that I'd need to use Quicksilver, I recruited him earlier so I could do Task 10 outside of Spec Ops.
After X-Ray was defeated to complete Task 13, and did another run through Mission 2 to complete Task 14. That's alright, as I need to have a Spec Ops mission open to spawn another Group Boss for Task 15. Then it was a matter of waiting until I had enough U-Iso to start the Research.
Interestingly, It is much easier to 2-bird X-Ray with Vector than to fight him with Vapor or alone. Using Vector to build up needed buffs on Black Panther resulted in an easy kill of X-Ray.
Ultron Prime Bug
At the point we start playing Mission 3, we need to use a work-around for the missing Ultron Prime boss bug. Ultron Prime is missing from the boss battle in Mission 3. If you fought and defeated each mini-boss separately, when you came to the Ultron Prime battle, you will see that there is nobody to fight. Only Vision as the team-up. If you try to start this fight, the game will crash. You cannot complete this mission if this happens. You will have to abort the mission or leave it until PD fixes this battle.
However, if you leave one or both mini-bosses around, then when you initiate the Boss fight without crashing the game. The mini-boss(es) will be present in the fight, but Ultron Prime will still be missing. At least you will be able to complete the battle and exit the mission. So the take away here is: If you 2- or 3- bird the boss battle, you can complete the mission, but so far most accounts from other players indicate that it will not count as defeating Ultron and thus not count toward Task 23.
Task 17-22 and Omega Task 4
There aren't enough Prime Sentinels in Mission 3 to complete Task 17 in one run. No matter, because I'll need to do a few runs of Mission 3 anyways. I've been running on U-Iso fumes now too. You will complete Omega Task 4 part way through your first run through Mission 3. Complete the first run through by 3-birding the Non-Ultron battle. This saves U-Iso and the two mini-bosses together without Ultron to help them is an easy fight.
After the first fight of your second run through Mission 3, you will have completed Task 17. Fight through and 3-bird the boss and use Vison's 4th power in 3 rounds to complete Task 19. (The 1-round cooldown only means that you can't use the same power twice in a single round if you have extra turns via Quantum Jumper or Cable's Temporal Shift, but in a typical mini-boss fight you'll have 3 to 5 rounds, so plenty of time to use Vision. Just have to keep him alive.) In a perfect world, you would do the Vision team-up against Crimson Cowl, then the Omega Sentinel team-up against Crimson Dynamo to complete Tasks 19 and 21, but because of the bug, you can't, so don't get stuck here.
Afterwards, you will need at least one other run through Mission 3. This time do the Omega Sentinel team-up mini-boss to complete Task 21. Now you need to make a decision: either 2-Bird the Non-Ultron battle now to exit the mission and work on getting more stars for the other missions or leave the last fight and wait until PD fixes this battle. Either way, you probably want to wait until you spawn another Group Boss to get 10 lockboxes to complete Task 22. Since Task 22 involves getting 5 lockboxes, I plan on waiting at least a day or two until after I defeat another Group Boss before I decide.
Task 23-25 and Omega Task 5-6
Task 23 is where we are all stuck. We can't complete Task 23 without Ultron Prime in Mission 3. If PD doesn't fix this battle or you don't want to wait, you can skip Task 23 for 10 gold. In that case, we move on to doing Epic Runs of Mission 1 to complete Task 25 and Omega Task 5. Doing additional runs of Mission 2 and 3 may be necessary for 4-starring all missions and completing Omega Task 6.
Boss fight in Mission 3 has been fixed. 2-birded the Boss fight that I left unfinished to complete Task 23 and already completed Task 24. All that remains is an epic run of Mission 1 for Task 25 followed by 4-starring the missions.