Rules you ignore/alter.

[Gumby Bush]

Originally Posted by kirbwarrior

I don't mind them using other things over it if it's part of the concept. One of my characters has a 'lucky ax' that he only uses once he's broken any better weapons in range. The ax is more of a good luck charm (with quirk-level delusion) than a preferred weapon and he'll still never go without it at his side.

On the flipside, I'm also entirely willing to upgrade signature gear as 'loot' for an adventure if it can make sense (effectively making the gear better by the amount based on loot they would have gotten plus the amount of money they'd get for selling it). This is especially relevant when enchanting is on the table, the PCs already want to improve this particular item over anything else for conceptual reasons.

I've also let characters upgrade their signature gear into either Ally (talking weapons!) and/or a special version of gadget advantages (the limitation is much smaller because it is assumed you will have it or get it back soon).

I'm with this. I use Signature Gear as perk (Plot Protected Item) and frequently build characters as having:
Signature Gear [1]; Named Possession [1]; and Weapon Bond [1].

I also let a signature gear item count as the gadget for gadget limitations. So, I currently have a character in the campaign I'm running with Alternate Form (Shark) with gadget limitations linking it to his (SG, Named, WB) fish hook... yes, the character was inspired by Maui.

However, I'm also happy to use The Captain's Boat (P3/71) and similar rules for Patrons in Boardrooms & Curia for large "Signature Gear" type things like spacecraft, abodes, etc. In fact, options like those (and the related "gear or ally?" puzzles) are what finally convinced me to switch, since the point values started looking skewed in comparison--it can be cheaper, otherwise, to have a tricked-out talking sword as an Ally than a regular sword as signature gear!

To the add to the thread: I tend to be quite charitable in letting players buy traits consistent with their concept. Occasionally, these are "oh, yeah, you probably should already have had that. Oops. Go ahead and buy it!" other times it's "yeah, I'm not going to bother making you do anything special to acquire that..." TbaM and WM are the notable examples here. I'd likely treat Talents and such similarly. Skills, spells, and the like I tend to treat normally, but if there's a skill which the player just didn't realize was needed--or where its complete lack from the party is causing issues--I'm pretty happy to let them buy it between sessions (e.g., Animal Handling (oxen) and Teamster after a session mostly consisting of chasing oxen, sometimes attached to a cart, around...).

I think it's standard practice, although not precisely RAW, to let players rejigger their PCs in the first few session as they realize what their purchases do. I have a player whose character has an Addiction. After realizing that it puts them practically unconscious for 2 hours at a time, we're looking at replacing that with some similar, but less severe, trait.