I think as we have seen with other ponies having the ability to do all sorts of things doesn't mean you'll necessarily be the best at it. We already saw Sunburst being way more knowledgeable about magical theory than Twilight, and Starlight Glimmer, despite being a unicorn, seems like a far better spell caster. We have seen Rainbow Dash be a far better flyer than pretty much any other pony in the series.
This is to say nothing of other non-pony species who we have seen some serious feats from. I mean look dragons, they are durable, most can fly, and they can breathe fire. There is even some evidence that they have some ability to cast spells as well. The only things alicorns have over dragons is a more control over nature (namely they can grow food?) and a greater spell casting ability, but this cost comes at being far less durable. Oh and they're not useless, as Spike is nearly tied with Twilight for the number of times Equestria has been saved, and he doesn't need a macguffin to do so.
This is to say nothing that due to the loose nature of the lore and the world, as well as applying some real world concepts to the mix, that alicorns couldn't be bested by some new concept that raises the power ceiling or renders their capabilities pointless.