Flame tank is countered pretty hard by Pitbulls and Attack Bikes (Air too) as well. They're completely different units, with their own strengths and weakness, however if you feel the need to compare the two, in terms of raw damage output and health, the Titan wins because unlike the Flame Tank that has high sustained damage, the Titan has high burst potential on a relatively short trigger. I'd rather not have units of either faction be turned into clones of each other that just look different.
Infantry units for GDI have always been a struggle when compared to playing NOD. NOD has a pretty solid line up of Infantry units that can deal with a wide selection of threats while not being vulnerable to those threats. GDI on the other hand, don't have any close the options NOD does for dealing with infantry, majority of units GDI uses against Infantry deal and take increased damage.