I had a similar experience with Tranmere Rovers in terms of the Barcelona-style football you referenced with Ebbsfleet FC. One of the regretful aspects of FM is that to enjoy a more difficult save, one must usually choose a club that is somewhat restrained in the transfer market and with the quality of players they have at their disposal, due to size and resources, as opposed to being able to find a deeper, more sophisticated tactical challenge in a higher/different league.
We've even seen teams like Rangers/Celtic hold a Messi-inspired Barcelona scoreless in CL games despite limited resources so as you quite rightly point out, a world class offense and tactically astute manager isn't always enough to easily break down smaller opponents. I've found that aspect of football elusive in FM.
Winning is fun, but I think from a purist point of view the holy grail is realism and being able to re-create real life systems in an FM match engine that is flexible enough to accomodate new, innovative ideas. In other words, give us the tools to show how good we are - and to allow the world class AI managers like Guardiola and Simeone to really separate themselves and show how good they are. It has to be a 2-way street or the game becomes unrealistic and too easy.
It's an interesting discussion as I think the overarching principles have been around a while and many of the new innnovations have simply been built on top of that, with roots in the ideas taught by Michels, Cruyff and Sacchi.
However, in terms of the complexity of the organisation, setting up the counterpress with positional attacking, methods to counter opponent dismarking measures, triggers to set up situational counterpresses to effectively force an opponent back to the prior transition phase, having situational and pitch geographic specific orientations in marking schemes, and the individual variations of counterpressing: man-oriented, space-oriented, ball-oriented and passing-lane, I think that has moved on since the 90's.
On some level, taken individually, all concepts have been around for decades (whether as a deliberate strategy a team trained for, or spontaneous, player-initiated action on the pitch) but as a collective whole and cohesive strategy across a wide range of leagues and teams, I think football has seen a change in the last decade as the coaching curriculae have improved and the younger coaches have infiltrated many more clubs, inspired by the likes of Sacchi and Lobonovski, Cruyff etc and looking to do even better with additional tools of analysis (e.g. video, tracking devices), better facilities (training pitch positional grids) and higher player/coach education throughout each club (now more widespread than the famous whole club tactical and technical philosophies that were once largely exclusive to Ajax/Barcelona).
I think it's largely evident as we see some of the older "world class" coaches become less relevant in the modern game. Keegan/Dalglish of the mid-90's in England couldn't get a job today (Howard Wilkinson on '92 fame I believe got Sunderland relegated after Peter Reid left) and Ancelotti seen as an innovator at AC Milan with his 4-3-2-1/4-3-1-2 struggles to really impose a tactical identity on any of his teams and largely has to rely on superior players dominating their league and man management techniques to get the best out of them. He more recently has taken over a more disciplined organiser (Mourinho, Guardiola), whose influence doesn't immediately go away, hence being able to still win things until that fades after 1-2 seasons. That's why I believe he hasn't lasted more than a couple years at Chelsea, R. Madrid and Bayern. Just my take on it, though.
I guess similar arguments for how football has collectively move on can be made for Benitez and Wenger, both seen as among the top innovators in the EPL at one point. It's not necessarily that their defensive schemes have changed or been degraded, it's more how teams defend against them, not just one or two teams, but the whole league can deal with the threats they pose/that were unique to their attacks when they first burst onto the scene.
Trapattoni, Capello, Hitzfeld, van Gaal, Hiddink, Boskov, Lobonovski, Antic - I'm not entirely sure these guys could get a top job AND be consistently successful in today's game, despite their obvious pedigree. All defended/marked/pressed in their own ways very successfully with varying degrees of depth and aggression but I'm not sure they possess the array of tools and complexity that we see at the top today. Could they learn and adapt? No doubt, especially with their skills and talent, I just think they'd do it differently to how they did it when they were winning in the 90's. Of course, I could be wrong and maybe my perception is off entirely.
EPL defences in particular had to adapt, as the prevelance of inside forwards became more common, to block those half-spaces the likes of Pires used to exploit so well.
Going back and watching old games, it is sometimes amazing to marvel at the space between defence, midfield & attack.
Until I actually went back and watched some 90's DVDs of Bundesliga, La Liga, Serie A and EPL (Football On Tap is a really good resource), I didn't believe the difference to today was so big. There were one-offs that were ahead of their time, absolutely for sure, but the leagues collectively have improved to a degree I didn't realise until I actually reviewed the old footage.
I think I have nostalgic memories of the 90's that sometimes clouds my memory of what the tactical organisation was like back then compared to now. At the time, it was the best I'd seen and things evolve so gradually over the decades that it's hard to remember just how much of a jump we've made in coaching quality over a period of, say, 20 years.
I just hope these ongoing changes in football are really tackled by SI to a much greater degree than they have been in the past as I don't think there has been a lot of innovation in the actual defensive strategies available to an FM game-world manager in the last decade. Has SI tried to improve the quality of defending that exists in the game? Sure, but I'm not sure that they've gone beyond that to really reflect the way defences are organised and used as an attacking weapon to disrupt opponents in real-life, modern football. FM defending feels very reactive and simplistic in comparison.
Just my view and insight into what my hopes, dreams and aspirations for change are when looking forward to the new FM18 release.