In my personal view, it depends upon how you value the looks and features. I like the looks of the regular old Drake (CST744E), and in the applications that we have it in two rooms in our home, I feel like it was a great, reliable, value for us.
We also have one of the CEFG toilets (meaning, respectively, Double-Cyclone Flush, Eco, Universal Height, CEFIONTECT) in the master bath.
In that room, it was worth a little more to have something that matched the pedestal sink we had, so we went with a design more like the Drake II (which was originally called something else when it came out recently-ish and then renamed Drake II, apparently because it was decided that it ultimately would be a worthy successor to the Drake. That's the CST454CEFG).
As to the features: The CEFIONTECT finish does help repel stains and resist skid marks, but I can't say I see them often on our non-CEFIONTECT Drake.
The Universal Height is a big deal. If you want a Universal Height (or ADA Height), i.e. higher, toilet, the Drake CST744EL is also available for about 20% of the price difference between the Drake and Drake II -- i.e. a little more -- while it is standard on the Drake II. I don't have a clear preference between the two heights, but I know some smaller women who don't like the higher toilet (although many females either don't care or do like it) and some men that really like it because it is easier to stand up, particularly if you are older.
The Double-Cyclone Flush is very cool. It rinses the bowl by swirling the water around from the top using two horizontal water jets under the rim. It's a more-obvious bowl wash, and that in itself may be a good feature because many people will look at the Drake and say that it doesn't seem to get water all over the bowl. There's a good test where you sprinkle pepper all through the bowl and then flush -- and, in the original Drake, all the pepper disappears. Then people say, "Oh." Both the original Drake (E-Max) flush and the Drake II (Double-Cyclone) flush are superbly-effective in removing waste from the bowl and not clogging in the "trapway" between the bowl and the hole in the floor where it exits the toilet. Indeed, the E-Max is a widely-praised and hard-to-improve-upon design in terms of getting stuff out of the bowl and down the pipe. The Double-Cyclone certainly does just as well, with maybe a little better bowl wash and, like I say, a more-obvious bowl wash. Both have a decent-sized water spot for a low-flow toilet.
If you like the idea of having a higher toilet and the CEFIONTECT, then the combo-pack of the Drake II, which incorporates both plus the Double-Cyclone, is a good deal. And of course aesthetics are a reason that a lot of people are willing to pay more for some things. If you don't like a higher toilet, then the Drake II isn't a good one for you.
So, that's the exhaustive analysis of the differences.
As you would see from the toilet reviews above (and the user comments), one of the great similarities between these two Drakes is how simple and readily-available their operating parts are. A solid, readily-available, and easy-to-replace valve that fills the toilet, and a flapper on the flush valve that is readily-available at Lowe's and thousands of local hardware stores nationwide. So every five years or so, you aren't faced with having to call a plumber or scour stores for some specially-designed part (as with the Champion flush valve). [There is a readily-available replacement seal for the Champion flush valve, but our experience on here is that people are having to replace them pretty quickly and they're often having trouble doing the the replacement themselves in the overly-complex flush valve. Also, on the Champion 4, it's worth noting that it has the same-size flush hole in the china as the Toto -- 3 inches. It just has a bigger hole (4") in the flush valve over the 3" hole in the china, which is of dubious benefit.]
Anyway, I hope this helps you to make a decision.