It's a very good case for mods. Compact but nice feel and light but adequate weight. Art Hong even makes a plexi for it! While it is shorter lengthwise than the HRAP's and TE's, it has fairly good depth (easily accomodates Seimitsu LS-32/-33/-40/-55/-56 series and JLF) and a good spacing for 30mm buttons. Button layout is very close nearly identical for the Viewlix configuration used on the TE and V3 SA/VX series joysticks. Very good space (better than most joystick bases) between the joystick and buttons. So yes, it's a very good case to do hardware mods and it will accomodate small PCB's (Cthulu, MC Cthulu, probably PS360) comfortably.
Doing a total hardware replacement on this case is, however, involved, and takes a while. You won't finish it in a day if you're careful. Plan for a week with plenty of resting. There's a lot of cutting to do!
I don't like the OEM joystick of the Agetec (at least as loose as stock JLF) and would recommend a JLF or Seimitsu replacement. IF the OEM buttons are in decent shape, they feel like but are not as sensitive as the Sanwa 30mm's. You can easily keep the original equipment and wire it up to a new PCB IF there's enough wiring to fit to the new PCB. There are diagrams in existing mod tutorials of what the signals/directions the original joystick wires carry (if you keep the OEM joystick). The Agetec buttons are easy to figure out for common ground and directional wires.
IF you do go ahead and do full hardware replacement (joystick, buttons) be aware you'll be cutting a lot of plastic.
You'd be best to follow these two mod tutorials to guide you ==>
http://burauzaa.com/joystick2/index.htm
and
http://shmups.system11.org/viewtopic.php?f=6&t=27126
Unlike MKL, I was comfortable using power tools (aka Dremel) to cut the plastic but you have to go slow. You can whittle down the "tunnels" of the original buttons with a Dremel but I'd use small files and cutters to create the mount area for your new joystick. Measuring and cutting for a new joystick are really critical for the Agetec case. The plastic is thin in areas and can get screwed up if you're not careful. Goes without saying that MKL's right about the mounting screws -- you really do need to get to M4 self-clinching (FLUSH) studs. Regular screws will split the plastic or destroy it over time which you don't want.
The trick with those studs is that most places will NOT sell them in quantities less than 1,000 because they're generally used for industry. However, if you check around you can sometimes find them in quantities of 10 or 25 per pack for a nice price (under $7) which is a nice deal. You really need more than 4 studs in case a stud gets damaged or lost. I kept my remaining M4 studs after my first Agetec mod and ended up using them on T5 faceplate mods, too.
I found the right studs here --
http://www.amazon.com/dp/B000FN12KE/?tag=neogaf0e-20
These are M4 threads, 0.7 pitch, 18mm length which is the minimum recommended. Any less than that, it'll be too short. More than that, you run the risk of poking into your Seimitsu PCB (if you get an LS-series joystick). M4 washers and M4 hex nuts (pitch 0.7) can be found at most hardware stores and Home Depot/Lowes. The studs are what you have to order online... Most stores just don't stock them.