I also have problems with gun cancel. It seems useless against anyone with fast moves (ie, ermac, smoke, teleporters, etc..)
That's why frame advantage is so important for Stryker.
I made a video about it a while ago but maybe it wasn't clear enough to understand. Basically, if you're going to use gun cancel tricks, ideally it should be when you have "speed advantage". If your opponent isn't doing anything and you take your gun out, chances are he'll just teleport or slide on reaction. BUT, if you knockdown your opponent, land a gun shot or reset your juggle then suddenly you have the opportunity to take your gun out before the opponent is even able to recover and respond with a wake up attack/reversal. Then you can use that to either zone, mixup, bait, mindfuck or whatever..
The most simple ways to set up safe gun cancels:
-After gun shot or grenade hits (if they block it you're in -frames).
-After ending combos with uppercut, standing 3 or standing 4.
-After Baton Sweep (gives more frame advantage than roll toss).
-After a successful throw.
That's when you should gun cancel or zone. When you're in speed disadvantage (-frames) you should be thinking about counter-zoning and reacting / dash blocking more than zoning and baiting.
Hope that makes any sense to you.
That's why Stryker is so hard to use properly. Not only do you have to keep an eye on both players meters and have excellent execution+reaction, but you also have to always keep track of frame advantage and have advanced knowledge of footsies and zoning.
But like I said, gun canceling is only really useful vs Stryker's BAD matchups (counter characters that can get around your zoning). You shouldn't even need it most of the time except to mind fuck the opponent and build meter.