As this is a computer game and not a real PnP session... You don't have the GM as a balancing factor. Instead you have to revise your mechanics to provide this variety of specialties at the same "costs" and then control encounters so the optimum specialty rotates in a balanced way (And control that the worse one still have a chance).
I will not enter into the encounters in detail because I don't want to spoil... That's why I focused on character creation flaws, instead... But D:OS can be improved on BOTH and, even if solo players don't need this adjustments (But I'm sure that they will welcome more variety in party tactics), multiplayer ones suffer when mixing characters "ways to approach combat".
It's worth nothing that if you had brought up the encounter design/balance you would have my full support, because it's to put it bluntly, horrible. And maybe this is what you mean when you say that mages dominate combat because magic is freely available, first strike issues, ignoring range, low AP costs for high DMG dealing, cool-downs, MASSIVE AOE and DOT effect stacking etc. This all combined makes mages very powerful. In general games often tend to go for either of 2 combat setups, strong main enemy with adds, or tons of adds as a group. What D:OS calls boss fights is how a well designed game and encounter should work most of the time.
Ps.: And yes, I should have clarified, I meant DnD 2/2.5 in 3/3.5/4 rogues are some of the biggest damage dealers and most versatile class. But it's a general theme in the later DnD revisions, classes have been boosted to stand their own in combat but also have support roles that they CAN fill.. I am not sure I like that more or less, no PC RPG ever ran with DnD 4.0 ruleset so far. And 3.5 was only in NWN2
Either way I wouldn't mind if a mod would change the balance to be more like DND3.5 or 4, but then also massively changes how magic works (uses per rest) this would limit your magic spam drastically, unless you cheese the resting system
Just to see how that would feel in actual gameplay.
But the core issue is the encounter balance, which basically requires and more than that, PROMOTES mass AOE/DOT elemental-chain spam. But It seems D:OS was made with that in mind anyway, and other classes are just.. uh.. bonus.
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... that's so far more than difficult enough for me !