Pug, one reason I go for Akropovic full systems is you can use them without any further mods such as Power Commanders etc and the bike wil still run fine. Saying that the bike should run fine too if you just fit end cans (not a full system)
The full system has noticeably changed the characteristics of my SP-2. No longer does it feel naff under 5000rpm as the exhaust along with the flapper mod has totally gotten rid of the big flat spot that was there.
With regards to compatibility if you are just going to fit end cans with link pipes then they must be for an SP-1. This is because the SP-2 has a different size bore for the manifold. If you are going to fit a full system then it doesnt matter as the mount points for the exhaust are exactly the same on the SP-1 as the SP-2.
After reading up many people rave about Sato's for just end cans. These are meant to be top notch quality though are rather loud. Think the info is on RC51.org or something like that. Dan Kyle has downloadable maps for these exhausts on this site. For just end cans though I dont think you will see much difference between any of the top manufacturers such as Akrapovic, Yoshimura, Sato, Arata (these I like too).
It's probably not worth fitting a full system, the only reason I did was because I got it so cheap off ebay! I was initially just looking to get end cans with link pipes as the standard headers are already stainless and the big weight saving is in ditching the exhuasts themselves. If I were you I'd just keep an eye on ebay for some 2nd hand cheapos. People generally take them off when they sell their bikes so I'm sure you will grab a bargain sooner or later

Be careful with some of the cheaper makes as its been that the packing gets blown out due to the V-twin pulses on those ones.
Of course to get the best out of the cans / system you should really fit a Power Commander. Saying that on the SP-1 its highly regarded as a 'Must Do' anyway due the the fueling setup being snatchy. Many people fit them even to their standard SP-1's to smooth it all out. They changed the setup on the SP-2 but its still not as smooth as the Suzukis I have ridden so I'm looking forward to getting my Power Commander fitted and setup. Should see the benefits of the full system too then. Totally standard my bike was making 124.5(corrected) hp @ the wheel so I should be seeing over 130 I reckon eventually. Though for me the best bit is the low down torque gain, its great!