Roast me all you want but I'll say it: SE is better than S2.

I have owned the SE and S2 models. The SE’s I have owned had better looking tops, more durable finishes, and were less expensive. My Korean made SE’s needed less fret work than the Indonesian made models.

On to the S2’s. They feel more comfortable to play and just play better. I like the bevel on the body much more. They needed zero fret work. It just feels like a better built guitar.

I’m on my last SE, which is for sale. Owned older CE models in the past. Those were sold off as well. Soon to be only S2’s in my collection.
I feel Core and SE are better than S2.

Except my satin Vela.

Well, that's because Velas are magical :).

In my case, I've owned several S2s (mostly Velas, but a couple customs) and a few SEs as well. I'm firmly in the "I prefer the S2" camp. Of course, my favorite guitar is well known to be the Vela, which only comes in S2, so that may bias my opinion a wee bit.

I will say that of the SEs I've owned, the Hollowbody II holds its own with the S2s.
I'm not sure which is better. I've only played SEs in the store. I've played a bunch trying to find one I liked. The only one that I liked and thought "I should buy one!" was the Silver Sky..... until I played a US model side by side and really felt like it was worth the extra money (used anyway). The SEs don't feel awesome to me and I find the tone a little muddy. I probably haven't played enough SEs to be fair.

The exception I find is the DGT. I played one side by side with mine, and it was pretty impressive.

I got a reward from work that ended up as a gift card to Guitar Center..... I bought a S2 Standard 24 Satin. It feels great, plays great, but the tone is a bit muddy and boomy. I'm hoping it's the electronics, but have been waffling on what to do about it, so it's been on the back burner since last summer.

As far as QC, any can have an issue. My DGT had a tuning stability issue when strong vibrato or strong trem use was applied. PRS took care of it though.... replaced the nut and trem and it's great now..... the S2 I have does great with this.
Roast me all you want, but claw hammers are better than ball-peen :p

The Hammer Of The Gods is my personal favorite.

I've played far more of all the lines than I can remember at dozens on dozens of music shops throughout the country, and experience after experience I'd swear you were talking about se not s2.

Don't get me wrong, I used to be solid in the se camp, and still think they're good guitars, but for a while now they consistently have the "objective" issues pointed out.. Especially the fretwork. Yet, I've rarely, if ever, come across a s2 with those.

As for the se sounding sweeter than core. I liked many things about the handful of seSAS I've played, but the one I seriously debated to bring home was quickly put to rest when I came home and played my core SAS, largely because of the tonal gap.

Again, nothing wrong with se, liking a line, or all lines. I know I like them all, but there's a clear distinction between each, subjectively and objectively. As there should be, otherwise why have lines?.
Does a core SAS have a bolt on neck?
I have no opportunity yet to compare the S2 and SE’s so I’ve no opinion on relative comparison.

But my SE’s are indeed great guitars. Inherent tone is just superb! If anything this thread illustrates the risk that PRS takes in allowing them to be so good. Whichever way the reality lies in a match up between S2 and SE, it’s great for us.

There’s little of that intentional downgrading for product differentiation at play here. We’ve all seen car model trims that are intentionally “uglified” to avoid cross cannivalising the higher trim.

Such a cynical act, isn’t it. Deny the masses a feature and reserve it for the minority, even though the feature costs nothing to provide.

The most amazing example is the SE swamp ash special. I could have sworn some of the figuring are as good as what I see on PSF! Crazy risk to take IMO, but hey perhaps that’s why I am not head of a successful guitar manufacturer.

The only flaw SE’s tend to have are nut slots that are not sanded or filed properly, lending to tune instability. Just want to be complete here. But that’s a simple fix with some sandpaper.
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I bought a S2 Standard 24 Satin. It feels great, plays great, but the tone is a bit muddy and boomy. I'm hoping it's the electronics, but have been waffling on what to do about it, so it's been on the back burner since last summer.
Have you tried adjusting the pickup height? A little closer to the strings could help with the muddy/boomy-ness. Worth a try before you dive into replacing electronics