Ok, let's leave the Krysae out because the weapon is an obvious problem, with or without TC.
Adjusting the boost damage duration only affects maybe the top few percent of infiltrators. IMO, the average Infiltrator won't be able to get the effect for the third BW/ Valiant shot -- not fast enough. You might say it's easy, but it still requires quick hand-eye coordination... A good number of people can't do it.
Essentially what I'll do under your suggestion is to shoot three rounds, two with bonus, reload and cloak again. Which is basically what's happening now with most shooters, my perception
The charged shot thing, is more about the way Bioware coded the tact cloak disengage. Basically, they tied the effect to "on trigger pull", not "on trigger release". Code change of tis variety can have some knockon effect so I'm not sure if BW will entertain considerations there. I don't disagree with what you propose, just not sure if technically feasible.
I'm not convinced boosting stealth is a good idea. The current level of stealth is fairly decent; bosses spotting you is reasonable for a boss level mob. Husks locking on though, might need to change.
Personally, I see most of the complaints coming from that the class is very good at dealing damage and there is no incentive for players to do anything else in game. Which is fair comment for bad infiltrators. To balance this, I prefer to see some tree options for builds catering to accomplishing objectives instead, as an alternative build.