Thanks, Bob; I took a look at what I have checked now under Look and Feel and Behavior Preferences, and don't see any I'd be willing to give up, so don't know if unchecking would speed up drops from BrainBox.
As for creating a new link between a thought and a pin, or another thought, I find it is nearly instantaneous, less than half a second. Don't know if that's a result of size of your super brain, but suggest you send request to Support, if you haven't.
You are correct that adding to the BrainBox on Windows PC is more of a pain, because it demands that you first open TheBrain on the web -- even if TB is already running on the desktop. (I just tried opening the BrainBox as a tab in the desktop Brain, and dropping link there, but it wouldn't respond to the drop.) So, for that reason, I don't use BrainBox to store from other windows on PC; would be easier, as you say, to just have an Inbox thought open in the Plex, and drop from another window in as a new child.
The beauty of the BrainBox is on iOS (and I assume, on Android too), where it is quick and easy to add links from other apps (except the Washington Post and New York Times), and it never says, "Wait, Open TB first!", and TB isn't running on the iPad or iPhone. Most of my links are added from news or articles I'm reading on my iPad or iPhone. (As I've written elsewhere, I really wish the BrainBox could be connected with IFTTT, which I use to automate shares to Evernote, Pocket, InstaPaper and my email, with one easy, fast two taps..
As for Lotus Agenda, I did another Google search to see if I'd missed anything new (no, I haven't), but came up with this old James Fallows article from 2009, where he bemoans the demise of Agenda, and others, but ends up saying TheBrain is maybe the best replacement available. Still true, I think.
Back in 2013, there was a brief hope that a project between David Allen and Charles Simmonyi and International Software would create a new replacement for Agenda, but nothing ever happened. I posted these comments and links back then to my Blog:
The "more" includes being chairman of a company, named Intentional Software, in Bellevue, WA, A year ago, they partnered with David Allen, author of "Getting Things Done" aka GTD, (GTD® and Getting Things Done® are registered trademarks of the David Allen Company.) The problem they seek to fix is that "Many GTD Enthusiasts today are constantly looking for new ways to incorporate applications and their numerous computing devices into their workflow." That's me, and maybe you too.
Unfortunately, they don't have the solution yet -- at least, I couldn't find it. So, I did a Tweet to the CEO, and hope I will be able to report some interesting things later. The tie-in here is to TheBrain software that I mentioned yesterday, which has the new version 8 beta now available for free download. (I can't stress enough that you need to take a look at TheBrain -- it could change the way you handle information for the rest of your life!)
Read more about Charles Simonyi and the GTD project at Intentional Software, TheBrain, and knowledge management at these locations: