As a bonus other thing I would like to see modified, I want to add more depth to Intermissions, and hope to make encounters in them as fun as the Operations themselves. That would make it possible to run games in the style of the Giant Robo OVAs or Xenosaga, and let you save up the giant robots for those times when you want to make the robots an occasional thing, to keep them special.
The Intermission system right now is fairly robust, which is to say it can do nearly anything elegantly with a minimum of complications, but suffers from being fairly bland. Skills are like Weapons, but without any of the special effects, and Traits are like Upgrades that cannot be enhanced. Item rules are almost nonexistant, and in fact are simply Traits with a few extra rules attached. I also am being very generous by calling that extra paragraph "rules".
The upside to this is that, as advertised, you don't need to refer to the book a lot to roleplay Intermission scenes. You don't need special rules to research a weapon capable of countering the enemy's latest gimmick, you can just roll an Extended Academics Test and you'll probably find something of value eventually, nor does social combat function any different from normal physical combat at all; You just tell people enough unsavory things until they break down like the bad guys from a series of videogames featuring Ace Attorneys.
There is nothing wrong with this per se, but with all the range of viable choices and tactical depth present in Operations, it is a shame that all you really need to solve any kind of Intermission challenge (whether it is social, investigative, a battle, or of some other kind) is a high stat first, an appropriate skill second, and a trait to help out possibly maybe as a tertiary benefit.
Now, there are limits to how much more complexity I want. As far as items go, I would rather not invoke the common "Inventory minigame" traditional to RPGs, with ridiculously long shopping lists of items half of which are never going to be relevant. Things like that bog down character creation too much in a game where you already need to stat up TWO characters instead of one, so they are going to stay as Traits.
That said, Traits could stand to be more like Upgrades than they are right now, for one they could scale and improve over time, for two they could have more interesting mechanical effects. Most Traits are tied to flavor right now, and they tend to provide an Advantage when that flavor makes them beneficial to you. Keeping in mind that GGG is effects-based and more about cinematics than realism, what Traits need is to be able to cover the kinds of of scenarios that PCs usual face (from diplomancing to treating wounds to hacking databases) problems in a way that is mechanically interesting without being tied to overly-specific fluff.
For example, a common problem with many games in which you are
expected to do investigation is that when the PCs fail their rolls to find a clue, the
game comes down to a halt until someone figures out a new lead. Many games with investigation as a central theme give people a chance
to automatically pass such checks at the cost of some other resource or a limited number of times,
in this way they help to keep things moving without necessarily needing
a derail of several hours to find another lead.
You can actually do this (or something like it) with the current rules, but by
making specific mechanics for investigative Traits we can make them more
interesting mechanically than, say, rewriting "Lucky" to apply only to
Investigation Skill Tests.
The way Traits would improve like Upgrades is rather
self-explanatory, an organization-themed Trait could be powered
up to have more retainers the more PP you spend on it, and a style of
martial arts will unlock the Secret Succession Technique sure
to destroy any who fights you after it is fully enhanced.
We note down the kinds of things that a character could want to do,
and make a category of Traits for each. Here's such a list, with a few
-Combat (For people who want their martial artist or sniper to be unique mechanically)
-Healing (Like Support Upgrades, but for characters)
-Movement & Vehicles (Vehicles that can emphasize terrain versatility, combat viability, etc)
-Knowledge & Research (Various ways to get clues from the GM)
-Allies (From having dozens of mooks to a singular ally stronger than you are)
This is only a sample short list, but I hope it gets the point across. I frankly have no idea if this is going to work out, but it could add a lot of fun things to do in the game beyond robots.