I think the Animus concept of it is what ultimately made the project be in development hell. It seems they didn't quite had the story bits down and game structure beyond the high fantasy medieval dungeon crawler exploration and, eventually, got canceled...
I'd probably play the shit out of it since there was a multiplayer focus compared to DD. Let's be honest here, Capcom could scrap the whole futuristic world concept and be only a medieval setting to be more marketable for the common gamer. However, I love how weird they can be and that's what I like about Capcom franchises...
Maybe? Personally, I don't think the story was the issue. There didn't seem to be a big investment of design and structure to the Animus-like future-NYC hub aspect of the game. (I don't think any of it existed in the TGS demo, you really only know there was this past/future sense to the game when you beamed into the world and the cavern rendered itself digitally before becoming rock and dust.) Capcom did release a shot of what the future world was going to look like, but it wasn't a compete world, more like an office space.
¡¡¡ÖCEDEC 2014¡×¤Ç¹Ô¤ï¤ì¤¿¥«¥×¥³¥ó¤Î¼¡À¤Â奲¡¼¥à¥¨¥ó¥¸¥ó¡ÖPanta Rhei¡×¤È¤½¤ì¤ò»È¤Ã¤¿¥¢¥¯¥·¥ç¥óRPG¡Ödeep down¡×¤Î¥°¥é¥Õ¥£¥Ã¥¯¥¹µ»½Ñ¤Ë´Ø¤¹¤ë¹Ö±é¤Î¥ì¥Ý¡¼¥È¤ò¤ªÆϤ±¤·¤è¤¦¡£¥«¥×¥³¥ó¤¬Æȼ«³«È¯¤·¤¿ºÇ¿·À¤Âå¤Î¥°¥é¥Õ¥£¥Ã¥¯¥¹¥¨¥ó¥¸¥ó¤Ë¤Ï¡¤¤¤¤Ã¤¿¤¤¤É¤ó¤Ê¹©Éפ¬±£¤µ¤ì¤Æ¤¤¤ë¤Î¤À¤í¤¦¤«¡£
www.4gamer.net
(BTW, theres a lot of interesting deep-dive tech stuff on that page about Panta Rhei engine that probably not many people saw before, with descriptions of its graphical systems and comparisons to similar engines of the time. It's not a casual-interest link, there's not much more you can learn about what the game was, but check out that link if you like tech talk.)
And this being some type of F2P multiplayer game, I don't think story was a main draw, outside of some lore associations. The original teaser showed a dialog sequence over a campfire (and also had different character classes beyond Knight) in addition to the Animus clue at the end (complete with anachronistic helicopter sounds which now make sense why there was a digital chatroom in a D&D-style dungeon crawler,) so maybe there would have been more interaction and storytelling, but none of that was in the demo and the "game" was supposedly going to ship the next year based on the demo's quality. (Then the next year Capcom said it had expanded the scope of the game, and from there it just got lost in development hell.)
My take on Deep Down was that it was going to be an almost arcade-like dungeon raiding game, or maybe at best early-Monster Hunter raids but in caves. You'd find three friends, you'd load/build up a dungeon map, you'd quest for stuff, and you'd take the loot back for next time.
I'm sure there was more to it, but in Ono's talks, it always seemed like he wanted a quick-hit, cool-looking launch-era game (and also a testbed for Panta Rhei) and he really didn't have in mind that scope for a full MMO or even PSO/MH-style set of words, it was more a replayable F2P experience. (The animus actually makes the storytelling a little easier, since core gameplay doesn't need to figure out how to place story details in a procedurally-generated world.) However, at some point in development they realized they needed more content for the F2P to work even on a small-scale basis, plus in the process perhaps they wanted started to think up more story to hook players beyond sheer combat, and it spun out of control from there.
...It was certainly a red flag though, that this cool-looking dungeon crawler game had this bizarre future-world hub to it. I remember there being a tangible "---Uh, Say what now?" when that became clear about the game. And that there was going to be some degree of storytelling but also F2P and multiplayer and randomly-generated dungeons, it didn't really add up to what gamers were saying they wanted. (Capcom is not a stranger to these sorts of F2P multiplayer adventures, but mostly that experience was in the mobile space, while its online co-op games at the time like DD Online and Monster Hunter Frontier / Online never made it out of Japan.) The press described the game as some mix of Dark Souls and Dragons Dogma, but as I understand the project, it kind of was more like an ultra-super-duper-fancy mobile game by design.