I have found the bow thruster on my 27OB to be totally inadequate for the waters we travel most and I started to look into a more powerful thruster. What I ran into was, cables to the thruster were not big enough for the increased current that the larger thruster would require. This would have been easily solved moving the thruster battery to the bow of the boat. On the other hand, while I have the equipment and knowledge to install a larger thruster, I am not in a hurry to cut up my boat to install a larger thruster. Typically a more powerful thruster also has a larger diameter prop and that means putting a larger hole in the boat to accommodate it.
If you were talking the stern thruster, then my concern would be, will the mounting holes line up or will you have to drill new ones. Again, will the power cables handle the current of the more powerful thruster?