I don't mind the questions at all. I hope you didn't want the TL;DR version.
Some of my pain points. Many probably have solutions, but I'm stuck between spending time dealing with it the way it is, and spending time finding a solution. These are not in any particular order:
1. Serial communication(terminal, for interfacing with console ports). I tried a few programs that didn't really work right away, and settled on Putty as that's what I used in windows. Except Putty under Ubuntu has no menu bar -- just an X to close it, and I can't copy or paste anything in or out of it. I also have to run it as root to access /dev/ttyUSB0 (I know I think there is a setting for this, just hasn't been important enough to spend the time looking). The copy/paste is the most annoying part.
2. Office(Outlook in particular) -- I tried a few options, even found a plugin for Thunderbird that would let me connect to an exchange server, but it just never quite worked right. I've adapted and am using OWA now, but I feel like it slows me down. I haven't yet been able to get Office >2007 running under Wine (not saying that I can't, just time vs benefit)
3. Google Earth Pro - I used this almost daily. I finally got it running under wine, but it's an older version, and many features don't work, such as searching by address. And any time it's running it leaves a shadow on the bottom of my screen, on top of all other applications.
4. Right-click shell interaction with 7-zip. Ubuntu's archive manager just doesn't seem to work right sometimes. I really miss right click > extract to ... or Extract all to (asterisk)\
5. PUTTING AN ISO ON A USB DRIVE. This is one of the more shocking ones and is something I can't even use the Windows 10 VM for because I'm not able to get USB passthrough working. Something as simple as firing up Unetbootin or Rufus and plopping an ISO on to a USB drive is nearly impossible on Ubuntu. I have Unetbootin, but have yet to get it to work. Haven't found Rufus yet for Linux/Ubuntu.
6. Network manager. It's always crashing and it never does what I want. Sometimes I just want to set a f*cking IP address on an interface and don't want to jump through 15 hoops. I might need to set addresses in 20 different networks in a single day. If I do it with ifconfig, the network manager "fixes" it for me. I have seriously resulted to using "sudo watch -n .2 ifconfig eno1 192.168.1.5 netmask 255.255.255.0" to set and keep an address on an interface.
Sometimes when it crashes and refuses to scan wifi networks(or 4g networks) I can just sudo service network manager restart, other times it takes a complete reboot.
7. I get random errors that pop up all the time "A system error has been detected, would you like to send a report to Ubuntu? With the default set to yes" -- never bothered to look for the error and it doesn't seem to coincide with any behavior I've seen.
8. RDP -- Remmina is pretty close to good enough, but sometimes I find copy/paste doesn't work, and the VNC function seems to have some compatibility issues.
9. CD/DVD Writing -- a problem solved long ago in Windows still gives me headaches in Ubuntu. System stutter will toast a disc, if I can even get it to burn at all.
10. Lock screen issues(not really productivity related...) Sometimes I will lock the desktop and close the screen(I don't often use standby) -- and open it back up and can use the desktop for 10-20 secs without entering a password. Then, as if it forgot, it will toss the locked screen up there and make me unlock it.
11. Task switcher grouping. I wish there was a way to turn this off without using the static application switcher. I alt-tab A LOT and don't like the delay I have to take in order to switch windows in a single application. To be fair, I hate the newer Windows behavior also that regroups windows in alphabetical order after the top few.
12. There's always some vendor rabbit hole that I get sucked into that would be easier to deal with on Windows. Maybe Dell packaged a bios update in a .exe file that can't be extracted without a Windows box(yes probably with Wine, but how much time am I going to spend getting that .exe to run?). Or some SAN management application, and don't even get me started on Java and Cisco's SDM, or some special VPN program I have to use to access a client's network that doesn't have a functional linux version, etc...
Those are the ones at the top of my head. I realize most can probably be solved with some time spent, but I'm still not yet nimble enough in linux to effectively compile/recompile things without following a step-by-step somewhere, and then when I do that, I'm left to my own devices to keep it updated, something I'd rather not spend cycles doing.
I'm running 16.04 LTS on a Latitude E7250 laptop. Chrome(not Chromium) is my main browser. There are tons of things that Ubuntu handles very well, and I paid nothing for it, so I can't complain much. One of the big complaint's I've heard about linux vs windows on laptops is battery life -- but I'm happy with what I get. Depending on what I'm doing, it will last anywhere from 2 to 12 hours. Standby and resume work well, though sometimes it seems that it shuts down instead of standby(though I haven't ruled out fat-finger in these cases), and all in all I think they've come a long way to making a usable OS for someone like me that's been using Windows since 3.0(though I'm quite comfortable on a command line).
As for the trust, it's mostly because I know TINSTAFL, and as it's free, I wonder where Canonical's interests are. The constant pestering to send error reports to Canonical are reminiscent of Windows trying to upload my crashdumps to MS. Whether or not these are memory dumps, I don't know, but to me Error report is often =Crashdump=memory dump= whatever info was in memory at that time is fired off to who knows where into an environment with unknown security.