I don't know if I call the lack of jumping much of a change, and it was replaced with that dash jump that IMO makes the game feel a little more intense. That being said bosses are easier than in Oath. I don't recall there being any references to the Eldeen, the story focuses more on Altago and its own dieties (which are completely unrelated as far as I can tell).
The skill system is a little different from the magics of the other games as well, but I don't think its so hard to get used to either. Then there are the EXTRA skills that act like stronger, but less frequently accessible sword magics from Ark.
I guess there are a number of small changes, but Ys games are always changing in one way or another. Ark uses a different magic system than I&II and Oath uses still another magic system. Older games use a bump system while newer ones are hack and slash. I think Falcom just likes to evolve the series as they see fit at the time, and I feel like it generally works for a very enjoyable experience.
Actually, nothing much has changed. the No-Jump goes back to the classics and the Dodge-Jump Works for platforming Adol's 3 Sword types from Ark was brought back as weapon classes upon that, there are no set amount of weapons/armor. The Party system is surprisingly Fresh with Circulating characters throughout the entire game Item Sythesis doesn't promote Farming since the items are in vast amounts as you kill monsters along the way. The mini-map was the best thing in Ys history, could have used that in solomon shrine all the way back in Ys II as For Eldeen References, I have a Thoery that the Inka Village is connected to the Eldeen for a few reasons. Story so far is really great
At First impression, I was a fish out of the water, almost hating the game, but after a little in, the game not only grew on me, its also building an impulse to buy the Vita just for the Ys IV remake!
Only thing I would add, Combat bonuses from Ys Oath and Ys Origin, That system makes battles alot more fun, and also drives you not to break that combo.
Every area was an Eyeful of Visual Candy, Knowing that there is gonna be a PC Port soon gives me Chills to think of seeing all those areas in HD.
Umm... I think it's allowed that once or twice we get a game that doesn't relate directly or indirectly to the Eldeen. There really isn't any reason to assume that there is a connection in Seven at this point.
As to the only other standalone game, I pretty much expect that Kefin's alchemy will be established as an attempt to either match or copy the power of the Eldeen when a remake of V rolls around but they could always leave that game an independent one as well.
As for the PC port, there's supposedly going to be a Chinese one now that ZnK's port is out but that wouldn't be a Falcom job.