This is a tough one to answer. They are two of my absolute favorite concealed carry and fighting pistols.
I do disaggree with NM_P99 on a couple of comparisons.
Using a post-ban 10 round magazine follower in a pre-ban full-cap p228 mag usually results in a gain of 1 to 2 rounds over the standard 13-round P228 mags or 15 round P226 mags that are readily available and usable in the P228. But still the P99 takes the cake here.
By technical box dimension the two pistols are nearly identical and the P99 measures slimmer but that's only because of the minor flare in the left grip panel of the P228 to accomodate the decocking lever, otherwise the P228's slide is measurably thinner than the P99's. I find the flare not to affect concealibility at all considering that all of my holsters carry this portion of the weapon above the belt line and thus is indistinguishable. One other note is that the overall length of the pistols are nearly identical but where the P228's hammer and grip tang account for the rear-most length measurement the full-dimensioned slide extends far back on the P99 to account for the grip tang. I find the extra slide length more fussy to conceal under a shirt, having a tendency to print or poke out more easily when carried in nearly identical holsters, on my frame (5'11", 195).
Although the P99 does have a lower bore axis it is not by much when you shoot high-handed as I do and is more than off set by the lighter frame and longer slide which changes the center of gravity on the pistol sharply upon recoil. I think the bore axis issue is over stated by many on not fully understood by all (no accusations here). Every person that has ever fired my P228 and my P99 has remarked that the P228 is far easier to control its recoil than the P99. The P99 simply exhibits far greater muzzle flip, the P228 is much more tame. I think that the few extra ounces in the P228s frame and its measurably lighter slide account for its relatively tame muzzle flip. Again, this is subjective, but no one that's fired both of my pistols has not remarked that the P99 has greater muzzle flip. I also suspect that David Olhasso wouldn't have achieved Grand Master with his P226 if the pistol exhibited particularly uncontrollable muzzle flip.
On the triggers, another subjective one. Both my two P99s and my two recent-manufactured P228s have equally outstanding triggers. It would be hard for me to prefer one over the other. No complaints here. All needed to smoothen up taken straight from the box to be as good as they are now. Lots of dry firing. I do prefer striker-fired pistols for lock-time reasons. I think the P99 does it better than any other pistols out there.
The P99 clearly has better trigger reset. In rapid fire drills I can shoot it fast but not any faster than my P228 while still remaining accurate and controlled. This is a training issue but one that favors the P228 as of late because it handles recoil far better and returns to target as fast as I'm able to reset the trigger anyways. I cannot get the P99 reliably back on target as fast as I can reset the trigger. Admittedly, I'm not the best at this skill.
Both of these weapons are super reliable and accurate. I've never experienced malfunctions with my P228 but have encountered the occasional cartridge that will not chamber in either of my P99s because of an overly long ogive on the bullet combined with the short throat of the Walther. Most notorious was the first-generation Speer Gold-Dot no longer in production. Like other polymer-framed pistols, the P99 will not reliably eject spent casings when fired with a limp-wrist. Although far better than my G17. I do have to barely be holding on to the pistol in order to induce these malfunctions (read: nearly flying out of my hand on recoil). It's nearly impossible to choke up either of my P228s doing this drill. For these reasons I favor my SIG by a small margin in its reliability.
Accuracy is very comparable. My instincts and experience favor the SIG here but the reality of the accuracy difference is so small to not really deserve mention. My guess is that the P99 will not suffer as pronounced accuracy loss when the round count reaches the tens of thousands. The P99 is simply more durable. Although, it's arguable whether you'll ever capitalize on this feature because if you maintain each weapon as they should they both should last for a very, very long time. Unmaintained the P99 is clearly more corrosion-resistant, too.
All in all, because of my personal shooting style, I ever-so-slightly favor my P228. It is proven and a benchmark standard for other pistols to be judged. The P99 is as close to dethroning my P228 as any other pistol has been able to come, and may someday do.
regards,
Tim