Strange that you mention MGS2's final boss, which uses a weapon you were already introduced to about an hour ago (and Snake gave you specific training for it, and it's one of the best weapons to use from that point on), and then praise MGS4, which turned into a fighting game with counterattacks and new controls while fighting Ocelot.
I think the final battle in MGS4 had a similar feeling of significance for me, since the music and method of combat changes in each segment to reflect a different game in the series (you could also consider it a callback to the final battle in MGS1). I enjoyed it, but I think ultimately it would have been better to finish with a gunfight like in MGS3 that utilizes the mechanics from the rest of the game (or series, for the same effect as the existing battle).
I never used the sword in the final segment of MGS2 (and I've beaten it on Very Hard!), and honestly had to stop and think back hard if you even get a chance to do so before the battle with the Rexes. If the game had taken away all your guns and left you with only the sword, it might've come across as less abrupt because then I would have had to use the sword through the final leg.
An unusual example of genre shift is Hydrophobia for the PC. The game is broken into three phases, each of which is clearly marked on the save screen. In the first phase, you have no weapons and solve the puzzles simply by running and climbing. In the second phase, you get a gun and wind up fighting a lot of foes with a combination of gunfire and environmental hazards. In the third and final phase, you get poisoned and have to search for antidotes, leaving you with time limits on many sections. At the very end, you develop water-controlling powers, which you use to battle the last waves of enemies and defeat the final boss.
It gives each chapter a different feeling, where you're slowly becoming more capable, but in more significant degrees than your typical JRPG or Metroidvania. In practice, it seems like the game might have been abruptly concluded and released with only half the planned content, since you are left unable to use your pretty involved powers in only a few rooms before the credits roll.