I think Thoughtseize is probably a good card to have in Modern, on balance. It actually makes it easier to allow a diversity of decks in the format: your fair deck now has a way to handle Karn Liberated and Desperate Ritual and Cryptic Command etc. without spreading itself too thin, so the format doesn't just devolve into decks doing their own thing and playing past each other instead of against each other. You could probably make a similar argument for Abrupt Decay. The problem is that BGx has not only the most efficient all-purpose answers in those two cards, but also a card that's far more oppressive (Deathrite Shaman), a very strong planeswalker that requires creatures to be able to pass the Jace/FTK test (Liliana), as well as the format's best creatures (Bob, Goyf, Scavenging Ooze). As a result, the best deck is something that's very hard to attack: the tool are there to stop you going over the top of it, but any attempt to engage it in a fair fight ends in your cards being outclassed. The decks that try to do this end up looking little better than Jund themselves - Voice of Resurgence into Loxodon Smiter into Wilt-Leaf Liege might *work* but it's nothing to get excited about.
Now, compare this to the format that most resembles Modern - the Mirrodin-onwards Extended format for the San Juan PTQ season in 2010. One of the nominal best decks, Zoo, resembled Jund in one sense - it was the most cost-effective removal spells backing up brutally fast creatures - but it was far more customizable than Jund is. The PT was won by Big Zoo with Punishing Fire, Green Sun's Zenith, and Baneslayer Angel; before long we had Boom/Bust + BBE Zoo, hyperaggro Zoo with Steppe Lynx, Blood Moon Zoo, Saitou's midrange Zoo list touching blue for Negate/Bant Charm, and some more obscure variants like Scapeshift Zoo. Zoo had a lot of strong cards but was much easier to attack than Jund is.
The other 'best deck', DDT, had more raw power than Jund - Jund can't kill you on turn 3 through disruption - but because it strength derived from the synergy between various interlocking pieces, decks lower down the food chain could compete with it by disrupting these combos. Did your Faeries deck not care about Marit Lage? All you had to do was pack Extirpate or Leyline for Thopter Foundry and you were good to go. Did your Elves deck not care about the slow inevitability of Thopter Foundry but worry about Dark Depths? You could sideboard Ghost Quarter and make a bad matchup passable enough to win a Grand Prix. Meanwhile, there was a variety of answers that hit both combos: Spell Snare, Celestial Purge, Bant Charm, Damping Matrix, Night of Souls' Betrayal, and so on. Nevertheless, you could adapt your DDT deck to stay one step ahead of the metagame and still walk into a tournament feeling confident.
Despite all of that, the current Modern format is reflective of a narrow conservatism and lack of vision. Jitte being banned is absolutely laughable. Thopter Foundry is more than safe in a format that now has Abrupt Decay, Rest in Peace, and Stony Silence, and a bunch of combo decks that couldn't care less about it. Green Sun's Zenith is eminently fair and would reward customization rather than the homogeneity we see in the BG decks. Ancestral Vision, as Zvi said in an article a while ago, is basically the Platonic ideal of a 'turn 4 format' card. Faeries is obnoxious but Bitterblossom is fine. Punishing Fire was't oppressive before and certainly wouldn't be now. Bloodbraid Elf and Wild Nacatl can come off for sure. Cloudpost is borderline, Stoneforge Mystic even more so, but I think both would ultimately be ok. It's not just the people making the banned/restricted decisions who are at fault here; there are some taken seriously in the community who actually want to ban Birthing Pod! Modern could be so much better, but I doubt it ever will be.
