In before “Why is Nihilanth such a moron that he actually sends you to locations you could not otherwise reach and that hold the secret to his immortality?? Balk Mesa SUCKZ!” x 50.000
For every type of end boss fight, there will be people who hate it and people who like it.
The HL1 boss fight, given the limitations of the engine, was all right – you had to use weapons and you had to use brains (realizing the crystals power his invulnerability), and you had to use skill (the jump and destruction of Nihilanth’s brain).
I’d recommend keeping these factors, but shuffling their execution a bit.