I've been playing 1E since Premier, and my take on the game is that while it's core design on release was solid, it was Decipher's execution that was flawed.
Chase Cards: In the first year of the game, most players focused on getting the
U.S.S. Enterprise and overpowered bridge crew in play, then plowing through dilemmas on high-point missions. It wasn't until AU and later that you started seeing Klingon swarm decks and other strategies become viable. In the best of worlds, obvious strategies for each affiliation - and cards to support it - should have been apparent to even casual players right out of the box.
Starter Decks: While the Warp Pack (which came out right before Alternate Universe) helped make Premier starter deck technically playable, out of the box starter decks for different affiliation did not happen until the Two Player Game in early 97 - and even then they missed the mark by not including a Romulan deck! Until then, you had to buy a starter deck and 3-4 packs (or another starter deck) to get enough cards to have a good chance at a decent deck.
Fixing problems by adding more cards: My biggest gripe. Professor Scott's post above illustrates how Decipher's approach to fixing problems was to add more cards you had to buy to address imbalance issues - instead of fixing or banning the offending card. Decipher steadfastly refused to errata cards and only banned one -
Raise the Stakes.
Creeping Complexity: Later expansions (i.e. First Contact and Deep Space Nine) added a welcome number of different play options, but also added sometimes needless layers of complexity. The Nor mechanics were needlessly cumbersome - particularly the Outpost vs. Station restrictions and ... don't get me started on sites.
With each level of complexity imposed on the game, the seed phase got increasingly complex. What started out as a couple of minute setup at the start of the game got more complex and convoluted, often becoming the focus of the game instead of ... you know, game play.
Looking back, it seems fairly clear that Decipher, particularly towards the end of 1E, was purposely cranking out expansions with very short playtest suspenses (full disclosure - I was a playtester for Holodeck and Motion Pictures). What we didn't understand until much later was how much the financial crisis Decipher was undergoing at the time aggravated the impact to their STCCG (and LOTR) product lines.
Sigh ...
On the plus side, I am encouraged by the CC's management of the game. They're not afraid to try new approaches with the game (my personal favorite is TNG Block "
Continuing Mission". Truly inspired), and are willing to review and adjust with errata and banning when necessary.