I don't think the first three seasons were a waste. I thought season 1 did a great job conveying a sense of the pioneering days of Starfleet, and recapturing the pure exploration that Star Trek was originally about. I felt it did as good a job in its own way of laying the foundations for the Trek universe as season 4 did. The difference is that S4 was focused more on interstellar politics and blatant continuity porn while S1 was more about the process of discovery -- both the discovery of alien worlds and interstellar politics and the discovery of the methods and practices of exploring deep space and making alien contacts.
One thing that I hope you do address is what exactly the aliens brought to the Federation and Starfleet and what they felt they got out of the union.
One of the things that REALLY bugged me about Enterprise was the fact that Earth was not given a unique identity and instead everything that was Starfleet and the Federation in the 23rd/24th century was assumed to have derrived exclusively from Earth. To me that creative (or lack there of) decision by the creators seriously undermined what unique institutions Starfleet and the Federation would become.
One of the things I like about both Babylon 5 and Stargate is that Earth ships essentially look like very bare bones flying bricks. They are not elegant, but they are what you would expect real world space craft designers to build. No frills ships that get the job done but have little concern for asthetics. On B5, once Earth joins the Interstellar Allaince, the ships progressively get sleeker and take on less of a flying brick look as they adopt more of the techology and design concepts of their alien allies (especially the Minbari and the Vorlons). The ISAS Victory and Excalibur look like what they are...ships built with the influence of multiple races. The same is true of the Valen later on.
The same idea was true on Stargate where the first USAF Space crafts were just blatant rip offs of Gould technology, and then they started to take on the contours or more human designs...and eventually incorporate elements of Tokra, Ancient and Asgard designs.
On Enterprise...everything about the NX01 screams that this is a basically a Federation ship. Hell Doug Drexler's upgraded season 5 NX-01 is a constitution class ship in waiting.