Factory Scheduled Maintenance

I have a 2008 VW Jetta 2.5 with a manual transmission. I bought it new and it has 65,000 miles. VW recommends certain maintenance procedures at certain mileages but all I have done is regular oil changes, faithfully I would add. Does anyone know of any issues that I may face by not doing the recommended maintenance plan? Or systemic problems with this model year?

After 6 years and 65k miles, you are overdue for a number of things.
You have the VW maintenance schedule in front of you and I don’t, so my list is probably incomplete, but you are overdue for at least the following maintenance procedures:
Air filter
Fuel filter
Brake fluid

The issues that you might face are spending money (often more than you saved) to replace parts that die earlier than they should have and getting stranded if you break down when you shouldn’t have. No one can say for sure. Maybe you’ll get lucky or maybe you won’t.

While your warranty was in effect, you also invalidated the warranty on the neglected parts, but I guess you got away with that.

Yes, don’t neglect changing the brake fluid. It absorbs moisture from the air and can eventually corrode the brake lines.

Find a recommended local mechanic in the Mechanics Files on this site. I would avoid going to the dealer if possible because (a) they will likely charge more and (b) they will likely tell you that (unnecessary) repairs are needed.

I would also drain and refill the power steering reservoir, easy DIY job.
Change the serpentine belt, cheap insurance.

Check your maintenance schedule in the glove box and see when VW suggests changing the serpentine belt. My 2005 Accord didn’t need it until I changed the timing belt at 105,000 miles. It wouldn’t hurt to inspect the belt for wear and tightness, though. Make sure you understand the brake fluid specs before you change the fluid. Use the exact grade required. This job is easiest if two of you work on it.

In general, you can neglect a lot of factory schedule maintenance other then oil changes and all filters if you plan to keep the car for under 10 years and 100 to 150k miles depending upon the car. After that, the next driver will reap the benefits. If it’s a car you plan to keep in the family and rust is no problem in the area you live, follow it to the letter. It does pay in the long run.

The serp belt on my Toyota started squeaking after 5 years and 27K miles, so maybe that’s made me a bit over-conservative.