Yeah - though they're more really like struts (the Devastator is an exception).
Starlancer improved on it a little (the ships actually have yokes! - no VDUs, though)... and that's about it. Everyone since then has been moving sideways - Freelancer regressed back to the cockpit strut style of Prophecy and Mechwarrior 2, while Mechwarrior 3 and 4 essentially fiddled with the Starlancer-style. All of them paint the HUD information as an overlay, though, which is kind of a shame; Interstate '76 had a great full driver's seat view where you could look at your speedometer and weapons indicator and they'd jostle around in true virtual-cockpit fashion.
(Honorable mention goes to Crimson Skies, which had excellent and readable virtual cockpits which I only discovered halfway through the game).
Still, if you look at the fan work being done (from Standoff to Hostile Frontier to Freeworlds: Tides of War for Freelancer or Mechwarrior Living Legends), everyone seems to want to bring back cockpits, and it seems like the older the game the more impressive work is put into it. Some of the Freelancer stuff is really good, and while I don't think Hostile Frontier matches up to Standoff's cockpits, that's still a gigantic leap over a game that had *no cockpits at all*. Mechwarrior is actually one of the bigger offenders here - I feel like they should be doing something amazing in that regard considering that they have the most modern game engine to work with.
The promo for the new official Mechwarrior game had some nice cockpits - but publishers squabbling over ports means that it'll probably never be released.