During the Steve Scott missions, Tommy is dead-set against featuring a giant shark in Scott's "movie" Bite, claiming that it wouldn't be successful. Then you realize that Tommy's been behind bars from 1971 to 1986, so he missed the release of a certain wildly successful 1975 movie featuring a giant shark, or at least the GTA equivalent. You can even hear him say "Who wants to watch a movie about a fish?" just after the first Porn Studio cutscene.
On VCPR, Congressmen Alex Shrub reveals that the government keeps prison costs down by letting criminals go free. The game begins with Tommy getting out of the jail, and he keeps getting off whenever he's arrested in-game.
Tommy immediately drowns when he falls into water like Claude and Toni. While those two were justified by the manual explaining that the waters around Liberty City are heavily polluted, Vice City shouldn't have that problem if the island spanning beach is any indication (in fact, Victor can swim just fine). Then, remember that Tommy has been in prison for fifteen years. Apparently, the prison didn't have a pool and Tommy fell out of practice.
There's also the fact that Tommy spent most of his life in Liberty City and most jails didn't have a swimming pool. So that could also explain his inability to swim as well.
In a few cutscenes - certain characters randomly comment on Tommy's "suit," no matter what you're wearing... Random unless you're wearing the Soiree (obtained in The Party), the only required clothes that fit such a description. This also explains why Ken gets upset that Tommy "ruined [his] suit" in the Final Battle: Ken is the one who recommended Rafael (the Soiree's designer) to Tommy.
The Prologue states that Tommy served fifteen years for killing about ten people, while during actual gameplay, murdering over half the city with a military helicopter that you stole can be overturned with a measly one hundred dollars. Easier to sleep at night by taking into account Gameplay and Story Segregation.
That, and the laws were potentially a LOT different fifteen years ago - since the earliest we see of GTA's Crapsack World is The '80s, perhaps law enforcement was actually somewhat stricter back in The '70s.
