Had both and find the 998 so much easier to ride as the bottom end is better as the engine spind up so much quicker than the 996 did.
The quicker spinning engine gets the power down quicker and allows you to carry the taller gear and still not have the jack hammer effect of the 996 at low revs.
Also never heardof any problems with 998 rockers flaking but the 996 has had bad reports from others for this.
Budget dependant the 998 would be my choice but the extra £1k is evident in the power delivery and also you get Ohlins rear tandard spec on the 998 bip as well as the rest of the 998 range but not the 996 until your in the s range.
I am now selling my totally standard 998 as I am contemplating a switch to track only riding for a year or so and cant afford to have it stood doing nothing anmd running the 748 as well.
Get a test ride on both bikes to see what I mean though, you will see the difference in power delivery
