The most significant difference between the 68k NeXT hardware and Macintoshes was that the former made extensive use of DMA, with dedicated channels for basically every peripheral and several "memory to memory" channels which are vaguely comparable to the "blitter" hardware in Amigas. 68k Macintoshes on the other hand are comparatively "stupid" and make use of programmed I/O for peripheral communication. (Heck, on early Macs and with regard to devices like floppy disk controllers you're lucky if I/O is even interrupt driven vs. cycle-wasting polling.) On a single threaded number-crunching benchmark a 40mhz IIfx certainly might perform better than a 25mhz NeXT Cube, you're basically just counting cycles, but a port of Next/OpenStep to the IIfx would by necessity have to waste a comparatively high number of cycles "manually" shoveling data around paths that are accellerated in the NeXT hardware so overall system performance would very likely be worse.
