Well... I have always had the philosophy that if it took you over a month to sequence a gene, then 4 hours in a computer is not an issue. However, in particular for times when people are using genewise simply to confirm that the a gene prediction is correct with respect to a protein sequence (sometimes the notional translation!) it is taking too long. In many cases you will know the rough region to compare the sequence to - if so use the -u and -v options to truncate your DNA at the correct points (the output will remain in the coordinates of the full length sequence).
For database searching there is the option of using SMP boxes efficiently with the pthreads port.
There are also a number of heurisitcs that use the BLAST program to provide the speed. These heuristics are found in the perl/scripts directory, called halfwise and blastwise and notes on how to use them are a later section (5). The scripts have extensive installation instructions, and I completely expect people to edit them for their system.
There is functionality for providing a heurisitic bound to the space the algorithm explores in the alignment. This is done via the potential gene option in genewise. It is not well tested out.