Well, this came out a lot more pleasantly that I, for one, expected.
I'll start by throwing this out there: I am pretty well in support of most of the things that Reika has done, including the old DragonAPI update marquee and the new popup. I feel like I'm in a minority here, but at least I am evidence that the minority isn't nonexistent.
Yes, the marquee was annoying, but it was there for a very good reason. I've only seen a fraction of the nonsense and vitriol that's been thrown in Reika's direction, and were it directed at me, it'd be more than enough for me to seriously rethink modding at all. Props to Reika for staying strong through all that.
The popup, I would say, is much less annoying. Among other things, it should let me take screenshots without having to go out of my way to edit the banner out.
I'm also fully in support of hooking into a version checker built into CoFH Core. I'd be wary about relying on NotEnoughMods, say, since I don't really have much reason to have that mod installed. However, I already have CoFH Core... so no problem there. There's a lot of modpacks out there that already have Thermal Expansion, and I'd wager that a good chunk of those that don't have Thermal Foundation for the worldgen configuration capabilities.
However, the main reason that I still have the marquee on my modified Infinity client is that updating mods is just annoying. When I load up Infinity+Reikamods these days (I'm current playing Pathfinder), it's usually because there's something in one of the mods that I want to test quickly in Creative mode. So I load it up, and when I log into the world a few minutes later, I get the marquee saying "DragonAPI is out of date! And RotaryCraft is out of date! And ChromatiCraft...". And then I'm like "Oh yeah, I should update those sometime..." And then I promptly ignore the marquee and never get around to actually updating, because I just want to see how quickly some Thaumic Tinkerer item can actually ruin a world and can't be arsed to close out Minecraft and update some totally unrelated mods.
So, I propose a solution: Make it possible to update the mods in-game. If I understand how Minecraft and Java work correctly, neither actually need the jar files after the game starts. So the outdated jars in the Mods folder could be disabled by adding ".disabled" to the filename, then the new jars could be downloaded directly to the Mods folder, so they load up next time the game starts. This could be added to the DragonAPI popup or the CoFH Core thing- preferably the latter, for compatibility with more mods.
All that would have to be made transparently obvious to the user, of course- if Reika just added an "Update" button to his popup with no explanation (outside of this forum/the MCF thread/the changelogs), I could easily see people complaining about "What if it the new update breaks my world? I want to be able to go back to the old version in case something breaks.". Something like "Click here to update <list of mods>. This will install <new versions> to your mods folder without deleting the old versions, so you can easily go back if something breaks. These changes will take effect the next time you open Minecraft." would do it. Better yet, have clicked-by-default checkboxes to each of the mods in the list, in case anyone doesn't want to update a particular mod for some reason.
If that's too much, at the very least, pop up a reminder when the client closes that some mods are out of date. A popup or chat message when the game starts makes me go "Eh, I'll do it later" and then forget about it. If I'm reminded when I leave the game (by, say, a "Some mods are out of date!" dirtscreen that lasts for two seconds when disconnecting from the (internal) server), I'd be much more likely to actually download and install the updates while I'm thinking about it.
Oh, and one more thing, this one more Reika-specific. I'd appreciate it if whatever notification (other than an easily-ignored startup chat message) didn't appear until, say, three days after the most recent version. I don't want to download DragonAPI, RoC, ReC, ChC, Geostrata, and ExpandedRedstone v7A just to download them all again tomorrow. With Reika's update cycle, this means that I'll just get the latest updates. Keep the chat messages for all updates, though (unless the non-critical ones are explicitly disabled)- I don't want to miss out on something cool in Botania or any other mod that updates almost daily, for instance.
TL;DR: I find Reika's notifications annoying, but still acceptable, all things considered. I think the best solution would be a simple way to update mods in-game, preferably built into either DragonAPI or a mod such as CoFH Core.