If there is a better way to finger that passage I don't know it - I can't even pretend to play the piece, after all (though I have certainly tried from time to time). Perhaps, as with the chromatic passages in 'Wilde jagd', the spirit of the run is more important than hitting every note on the way up (or down in the case of the Liszt)? I can say it's somewhat easier to play the analogous passage on the violin in the orchestral ritornello, but that's because it's just six notes of an ascending D melodic minor scale.

(Incidentally, the passage immediately preceding said scale in the ritornello is one of my favourite in the entire movement - indeed, in all music. In fact, the first movement contains at least four or five of my favourite moments in all of music and many others besides that I love to hear each time they come around when I'm listening to it.)
As for the Alkan Grande sonate, well, the first movement is as much a part of the overall progression of the sonata as the last movement - just as 'Promethee enchainee' is extremely slow, heavy, and plodding to depict Alkan's idea of 'old age' (insofar as 50 constitutes old age), so the first movement is a frantic whirlwind to depict the energy and hedonism of youth (the excesses of which catch up to the subject in 'Quasi-Faust', I suppose). Granted, the material from which he spins the scherzo sections is of relatively little intrinsic interest next to the rest of the sonata (creative use of hemiolae notwithstanding), but I don't know that I'd say it doesn't work in the context of the piece as a whole. The piece as a whole, after all, is meant to depict the slowing down that comes with growing older, and to spin this out over four movements so that there is a noticeable drop in tempo at each stage he needs to start with an extremely fast movement - and conclude with an extremely slow movement, which, though I agree it is a unique and powerful way to finish the piece (especially the muted final chords, which seem to imply that the anguish of the preceding bars carries on after the piece is over), is rather different to the usual upbeat conclusions to pieces in four movements, and since the third movement is also on the slow side, it probably confuses more people than it reels in. Perhaps this is why 'Quasi-Faust' is usually played alone?