I am working on figuring out what quests can be 'missed' as you adventure about. I thought I'd report them here in case anyone has any interest. I am not very fair in this 'project' at all so it's a skimpy list so far

Khenarthi's Roost
Be sure to complete To Auridon before working on main story line in Auridon.

Auridon
Missive to the Queen-This quest is only offered if you have not completed Ensuring Security.
This quest is mutually exclusive with All the Fuss.
All the Fuss-This quest is only offered if you have not completed Ensuring Security.
This quest is mutually exclusive with Missive to the Queen
Back to Skywatch-This quest is only available if you have not started Lifting the Veil.

I grab Back to Skywatch and either Missive or Fuss before questing in the zone.

Grahtwood

This is awkward and there may be a better way but...
In Auridon accept the quest the Great Tree. Take boat to Grahtwood and complete Unsafe Haven.
After completing Unsafe Haven, delete Great Tree quest. Go get Trouble at the Tree.
After accepting Trouble at the Tree, return to Auridon and re-acquire The Great Tree, get on the boat and when in Haven, just hop off the boat and go on your merry way
Brackenleaf's Briars-Complete this quest first then Bosmer Insight. Quest giver is in Southpoint.

Not quest related but for lore reasons....The Unquiet Dead-do first for lore reasons then do Eyes of Azura.

Greenshade

Aid for Bramblebreach-Do first
Breaking the Ward-Do before Retaking the Pass or Shades of Green or The Blight of the Bosmer. I usually grab this quest when I first enter zone but don't work on it until you complete Naemon's Return. You can actually do it earlier but it messes up the lore of the story since it talks of the Prince being a liche before that part of the story evolves that way.

The Senche-There are several hunting quests. If you do this one last it feels better lore wise as each of the hunters goes on and on about the quest giver in the Senche so it's nice to do him last.

Malabal Tor
This is where I currently am so will add more things later
The Siege of Velyn Harbor-This quest only offered if you have not started House and Home. So, grab it before you quest in the zone.

Wrothgar
Do this after finished main storyline for lore reasons and a special appearance of an old friend

Alik'r Dessert
Tharayya’s Trail: You will no longer be eligible for this quest if you have already completed Volenfell and the quest Blood and Sand

Shadowfen
Bound to the Bog-missed this quest on my first run through. When I get there next time, will figure out what needs to be done to make quest appear