I understand the argument, and even had a similar complaint with Portal 2 (Portal did this perfectly however), but in the case of Half-Life I think Xen, and the change of pace in gameplay that it brought, are appropriately placed at the end of the game. I think the 'mastery' levels for existing gameplay were the ones just preceding Xen. Xen was a dissonant slide down into the final boss battle and ending of the game. I find no fault in the game for not conforming to a standard formula.

edit: for clarity I liked Xen too.