Do you have any instruments on the boat now? If you do, you may want to look at an auto-pilot by the manufacturer of those instruments. Most newer instruments should be NMEA 2000
or 0183 compatible, so in theory it doesn't matter. I've found that it is sometimes easier to get support when all are the same. I wouldn't let that be an overriding concern, but it is something to consider.
Also, how old are any instruments and/or chart plotter? You want to be sure that they will work with any auto-pilot you buy.