Depends on what you compare. You're probably already aware of everything below, but I'll repeat them for everyone's benefit.
(1) All 250 SE coupes were "high grille", 6-cylinder versions, with 4-wheel disc brakes, lots of bling (more on that later).
(2) Early/transition 280 SE coupes were "high grille" ("Hochkuhler"), 6-cylinder versions.
(3) Then came the 280 SE coupes with a "low grille" ("Flachkuhler"), both in 6-cylinder and V-8 configurations.
If you compare (1) and (3) for the 6-cylinder models, sellers seemed to be emphasizing the "low-grille" aspect, which I found very odd. From an aesthetic point of view, I much prefer the "high grille", as that is how the car shape was originally designed. I know there are some who care about getting the "low-grille" version. To me, these idiotic preferences present an opportunity to get a better deal on a "high-grille" version...
If you compare (1) and (2), I personally didn't see any noticeable price difference. There is always that contingent of people who will place a premium on the last model of a given line (same reason behind the irrational price premium of 280 SL over 230/250 SL).
If you don't care about re-sale value and appreciation, then, ... wait for it.... "buy the best car you can find." The old saying is especially apt for a 111 coupe, as the sheet metal and chrome pieces are horribly expensive (if you think a pagoda is bad...). The drive-train is identical to the corresponding sedans, so mechanical spare parts are relatively abundant.
At the time I was searching, I concluded that I needed to find a car in cosmetically great shape, but mechanically so-so. Which is what I ended up with. I've since completely over-hauled most systems (brakes, power-steering, cooling, heating, suspension), as everything was in poor shape. The previous owner had spent more time and money on new rubber, re-painting and re-chroming... which was fine by me!
Regarding personal preferences on the "bling" of earlier models: same arguments transfer over from the pagoda discussions (outside mirrors, inside door hardware, chrome vs. aluminum trim, etc). In addition, the wooden binnacle that Wallace has already mentioned, as well as general quantity of wood on the interior. I
very much prefer the earlier models. If these things don't matter much to you, then I would say buy the car that has less rust and better chrome. (watch for dings on the long chrome pieces that run the length of the car, under the doors. Not cheap, and unavailable)
There's nothing like cruising down the highway with four-on-the-floor and the sunroof and all 4 windows open in a pillar-less cabin wrapped in leather, wool, wood, and the shiniest chrome for miles. Who needs a convertible?