I spent a bunch of time at the Residence Inn just off Butler Blvd on the other side of 9A. While that hotel hasn't been remodeled in a while, I always felt the staff did a great job of keeping it clean and well maintained. A few minutes away is the St Johns Town Center and that is a great time waster if you are looking for one.
One note of caution. The hotel is on Deerwood Park Blvd. Weekdays between 4:30 and 6:00 you will need to budget extra time (extra 15 minutes) if you plan to travel towards Gate Pkwy and the 9A entrance.