This may be a very arrogant statement, but I'll say it anyway.
I'd take a T5 anyday over any TKO, TKO II, 3550, T45, or T56. Of course this is just in my case in my H/C/I car. In a high(er) powered situation, I'd use either a G-Force or a Pro-shifted Liberty T5. When I blow the 2-3 cluster out of my car, I'll pull the trans out, rebuild it in 2 hours, and have it back in the car. When you blow out a 2-3 cluster in a TKO or any of the other transmissions named above, and you'll won't have your car for the next week, and the "mod fund" will take a serious hit.
Sure, the T5 is inherently weaker than any of the other transmissions above, so why would I stay with the "weaker" T5? Simple - the T5 isn't weak. For 99.5% of Mustang drivers, a T5 is more than enough, and why spend the money for a "stronger" transmission when it's not needed. Spend the 300 bucks for the new synchronizers, blocker rings, shims, races, springs, thrust washers, snap rings, etc. and call it a day.
Again, this is just my opinion. Filter through all the BS about T5's being junk, and plan ahead. If you are going to build some wild race 347 motor, then yes, a stronger transmission is probably in order. However, if you are going to be staying with the stock shortblock and no serious power adder, the T5 is more than enough.
Joe