Like many others, I've ran into issues with loading more than a few mods at a time due to the Skyrim SE bug which can limit you to installing 5-10 at a time, launch & quit Skyrim SE, then load 5-10 More, etc...  So, if you're running into that as well, this should help to make installing 5-10 at a time easier as you won't have to manually copy and paste the load order every time. (Note: Please be sure to read the warnings below)

This is a Simple Batch file which DELETES your existing Skyrim SE "Plugins.txt" file for Skyrim SE and then reads the MO2 "LoadOrder.txt" and writes all but the first 6 lines of the Load Order.txt file to the Skyrim SE Plugins.txt file, adding the asterisk * for each esm/esp entry listed. (Note: The first 6 lines in LoadOrder.txt are the "File Created by Mod Organizer" remark and the Main SSE Game & DLC ESMs which are not used in the Skyrim SE Plugins.txt file normally)

Here's excellent & expanded description provided by AsatorThundrGod in the posts section: (to which I am grateful for the assist)
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MO2 doesn't update the Plugins.txt file which SSE uses to control plugin load order & activation. What that means is after you install your
mods in MO2, sort your load order in the right pane, and launch the game, SSE doesn't know or care what your MO2 load order said; anything
that wasn't already activated in-game previously will be deactivated, and anything not 'active' will be alphabetized. So you have to re-sort
and re-activate every new plugin, every time. This gets old pretty quick. Also when you exit the game, your right pane of MO2 will be
alphabetized, which I don't think actually "matters" per se, but it's misleading.

If I understand the author's intention here, it's a BAT file that you run after each time you change your load order in MO2, to force the game's
Plugins.txt to match what MO2's load order says, both for load order and which plugins are active (though as his warning states, it will assume
any plugins listed in MO2 are all active). It adds an extra step before you launch the game with a new load order, but should save a lot of
aggravation.
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As I've used this more and more, I've learned that it doesn't matter if you use MO2 with Bethesda Mods, so you can disregard the warning about them being overwritten.  If you can see them in MO2, they'll be applied to the Plugins.txt file along with the MO2 loaded mods, however it still WILL NOT differentiate the active versus inactive mods... so the warning in the yellow text below is still accurate.

WARNING:  I do not know who would be using BOTH MO2 and the in-game downloaded Bethesda Mods for Skyrim SE however, if you do, DO NOT USE THIS BATCH as the Mods from Bethesda are enabled and listed in that Plugins.txt file.  Those entries WILL BE DELETED when the Plugins.txt files is replaced.  (The Plugins.txt file references will be replaced, not the physical Mod Files in the Skyrim SE Data Folder) I'm won't be held responsible if you've downloaded some mods in-game as well as are trying to load some mods via MO2 and end up not seeing the "In-Game" mods you downloaded!

Also, as this method currently has no way of "sensing" which mods you have Active and which Mods are listed in the Load Order but Deactivated (i.e. Not Checked), PLEASE make sure you ONLY have the active ESMs and ESPs you want to load showing in your Mod Organizer Load List.  I currently haven't found any way to detect which ESMs/ESPs are Active and which are listed but Inactive. (They're not tagged in the MO Load Order File, that I've found.)
In other words: Double-Click each Mod you're using and move any InActive ESMs/ESPs, you do NOT have checked in your load order, to the "Optional ESPs" section of the mod to remove them from the load order entirely or they will be activated by this Batch.)

Addendum: I haven't been unable to get this working as an MO2 shortcut yet... but  I haven't given up, I just haven't had time to delve into why it won't write the Plugins.txt file when launched from within MO2.

Instructions:
Extract the Zip to some location you'll remember. (just contains the batch file "Sync_Plugins.bat")
Copy the "Sync_Plugins.bat" to the Profile folder of the active profile you're using in MO2.
Create a shortcut on your desktop (or wherever you want to have quick access
to the batch while in MO2 (don't try adding as a binary in MO2, I've
tested this and it doesn't work when ran from there for some reason.)

Now, Launch MO2, Sort your load order however you want it, then Double-click the "Sync_Plugins" shortcut you created... then launch Skyrim SE from within MO2 and you should see all your mods loaded.

Update 11/14/2016:Just changed the title so it would group with other MO2 files.
Update 11/18/2016: Added Orange text to description and ran  a strike-out through the red text warning, added addendum about using in MO2

I've never posted anything to NexusMods, so I'm not familiar with how all of this works... however, I've used hundreds of mods from here so I thought I'd give something back.

Endorse if you like it... or don't, it's up to you.  And if anyone would like to update this/improve it, feel free to update and repost to NexusMods or let me know what you feel could/should be changed and I'll update and repost with the changes.  If you repost elsewhere, please just reference me as the
creator... I get so little love from the outside world. :)