1) One of the advantages of a desktop over a laptop is that you can add on cards. A PCIe SATA controller can be had for $20-$30.
2) You can always use the Intel SATA2 ports. Contrary to popular belief, SATA3 doesn't really give you that much extra compared to SATA3. Certainly not double the speed you'd expect if you're looking solely at max MB/s.
First, yes the sequential MB/s numbers are a lot bigger, but they're the inverse of wait time so each doubling of MB/s gives half the reduction in wait times. In other words, most of the reduction in wait time happens at
low MB/s figures. e.g. If you're reading 1 GB of sequential data, compared to a HDD:
10 sec = HDD @ 100 MB/s
4 sec = SATA2 @ 250 MB/s
2 sec = SATA3 @ 500 MB/s
SATA3 saves you 8 sec compared to a HDD, SATA2 saves you 6 sec. So in terms of wait times, SATA2 is giving you 75% of the speedup from a HDD compared to SATA3. That's totally unexpected if you were comparing MB/s assuming it was proportional to time saved. PCIe SSDs give you even less of a speedup than SATA3, and I would advise just skipping it unless you can get it at essentially the same cost as a SATA3 SSD, or if you're doing real time video editing (which heavily stresses sequential read/write speeds).
Second, because MB/s is the inverse of wait time, the SSD spends
more time doing tasks with
low MB/s. If the drive has 500 MB/s sequential reads and 50 MB/s 4k reads (30 MB/s is more realistic, but I'm trying to keep the math simple), and you give it a 1GB sequential and 1GB 4k (small file) task, it will take:
2 sec = 1GB sequential @ 500 MB/s
20 sec = 1GB 4k @ 50 MB/s.
22 sec = total time
So the drive only spends 9% of its time taking advantage of SATA3 speeds, and 91% of the time it's not at all limited by SATA2.
So SATA2 isn't really that big a hindrance to a SSD, and is a viable option if you're planning to update your computer in 1-2 years (at which point you can transfer the SSD to the new computer). Here's a TomsHardware test on it. Pay particular attention to the real world tests.
http://www.tomshardware.com/reviews/sata-6gbps-performance-sata-3gbps,3110.html