There is a fairly significant difference in the hullshape - the Series IIs tend to be better sea boats and a bit more efficient, but the older ones aren't bad!
I prefer the layout too - its a personal thing. The Series II 45s were Galley down and port, with a midship master (either double or twins; the double is IMHO the better setup) and a forward V-berth. A single head was most common although there were a few boats made with a second head in the V-berth - I have a friend who owns one and I can't imagine why someone would order that, to be honest (a head right next to where you sleep, in the same compartment?! No thanks!)
The ER on the Series IIs is a bit tight, but not intolerable. The batteries are aft of the bulkhead under the cockpit sole, which is an excellent location for them. I HATE batteries you can't get to easily. My only real complaint with the ER on the Series IIs lies in the AC compressors (outboard starboard) and the water heater (outboard port.) The head system is Vacuflush and "just works" as stock - although some people have butchered them (which IMHO is a HUGE mistake!)
The cockpit is very fishable, the bridge well-laid-out. I can steer with my feet, which I like to do on long cruises. The instruments are all visible with no sight-lines blocked. Sightlines forward and aft are excellent from the helm as well. Everything "just works" in terms of how the boat is laid out and how things flow - you can walk around inside her at night and not bang your head or trip on something when you need a soda at 3:00 AM.
To give you an idea how sound the basic structure of these boats is the Series II 45Cs have two struts - an intermediate and then the one at the prop. This is great if you have good hull stability (lots of support for the shaft) but an utter disaster if not, as with that much stability in the shaft if things drift you will DESTROY transmission bearings.
When I bought mine the cutlass bearings were documented as having been done about two years prior. During the entire time I owned the boat they NEVER needed ANY attention whatsoever - when I was out prior to selling her they were still nice and tight, and on survey no trouble was noted! That's seven years - and that boat was NOT a dock queen during the five I owned her!
Over the entire time I owned her the total alignment drift was six thousandths on one engine, four on the other. That's impossible to argue with in terms of structural stability.....
Oh, and here's another one - other than some stress cracks around the half-tower mounting legs on the bridge, my boat had ZERO cracks anywhere else. Not in the deckhouse, not in the corners of the deck, not where the gunnels and deckhouse sides met, zero. Anywhere. At all.
Perhaps the biggest "gotcha" with them is that virtually EVERY one I've looked at (and this includes some Series Is as well) which had a pulpit on it with the windlass had the windlass and pulpit improperly bedded. EVERY ONE! Now I'm sure I didn't look at them all, but I rejected TWO when I was looking that had obvious problems in this area - and later discovered mine had trouble too, but it hadn't gotten beyond the backing plates where I could detect it yet by sounding when I bought it, and as a consequence both I and the surveyor missed it. This was a MAJOR job to fix, and the previous owner of mine KNEW there was trouble in there as he ran epoxy (!) into the gap between the pulpit and the deck - this I discovered when I tried to dismount the pulpit, and wound up having to use prybars and chisels to slowly cut away the joint! NOT fun.
Since I fixed mine I've checked a friend's (his has trouble but he's taking a trip on the river "de-nile"!) and I know of another that was at my former marina that I also checked for its owner and it too had trouble there. I'd say expect trouble in the forepeak area and hope it hasn't gotten beyond the bulkhead - if not you can fix it from the underside which is less intrusive, although either way its a ROYAL biatch of a job (see my thread here on it.)
I would INSIST on pulling one of the windless mounting bolts during the survey/inspection process and probing in there with a pick or some kind of tool, or using a relatively-high-powered light to have a look-see at what that hole looks like. If the pick comes out wet - and its a good bet it will - you've got big trouble down the road..... Exceptions made for those who have already fixed it, of course!
IMHO a "nearly ideal" boat of this size and type would be a Series II 45C that had tired (or dead) engines but was structurally sound. I'd take her and repower with either QSC-540s or, if you're a speed demon, QSM-660s. Either will fit - the QSCs will give you a LOT of room and a modest speed improvement (~20-22kt cruise, 25ish at the top) while the QSM-660s will easily break 30kts. Both will result in a MUCH more social (quiet) boat, cut fuel burn by 20% or more at cruise (I know someone who did this, and I couldn't believe his fuel numbers - with the QSMs he was seeing 36gph at 22kts, while I was burning the same at 18!) I'd probably go for a total refit on the cosmetics too, and get rid of the sliding door (which I personally hate - the lower track traps water, even with the weep holes, and the bulkhead invariably gets damaged as a consequence) while I was at it.
You'd spend all-up about half a mil doing this, but you'd have a boat that IMHO would blow away anything from the production builders of today, and it would have the timeless lines of the Hatteras. I'd put the Hatt's seakeeping up against anything out there in today's "newfangled" boats when things get nasty. Total investment would be just under half of what a "new one" would cost, which would pay for a hell of a lot of fuel, dockage and insurance.....
I really appreciate your time and expertise. That's why I luv "boat people". Too bad for me, ya don't live in Jersey, cause I could give you a full time hobby, after I find my Hatt. 
