SGP does have its limitations. This is mostly due to the fact that it is designed for astrophotography rather than photometry. For example, if I want to do three sequential runs of M67 for BVRI, I have to program in M67 three times (M67-1, M67-1, M67-3) rather than simply telling the program to recycle. Fortunately, it is easy to do the replication. Also, you must watch the options for repeating within a single target plan. Finishing all filters is the default (BBB, VVV, etc) while we photometrists would cycle between filters (BVBVBV, etc). At least once I forgot to change that option and ended up with a four hour run of "B." Again, SGP is designed for AP so you need to work with it a bit.
I find SGP's target generating plan, plate solving and PhD2 integration handy enough to override the above limitations(and perhaps others). Further, the cost/benefit ratio is outstanding. On a typical night I:
(1) slew the scope from park to one hour west of the meridian.
(2) plate solve to insure that the mount know where it is in the sky. (Is this really needed? I consider it a sanity check.)
(3) open and check PhD2 for tracking and adjust if needed.
(4) Get an approximate focus and then run the focus routine.
One tip: For the centering routine do not try to center to the nearest pixel. SGP will try to do that, but it will take many plate solves. I would have to check, but I think mine is set on 50 pixels as "good enough." As I use VPhot and LesvePhotometry, both of which plate solve each image, I don't worry about aligning images.
Since most of my runs are on EBs and are typically 3-4 hours I take the time to center the target and re-check PhD for guiding. Then I begin the run. After initially staying up all night I found the routine safe enough to hit the hay as SGP automatically stops PhD2, parks the scope and warms the camera. As it directly communicates with our weather station I don't worry about the weather as all will be shut down if needed.