We have lots of changes in our campaign, not all would be good in a vanilla Ars setting. Among the things that could be used are as follow:
The most important thing
Parma Magica needs to be changed IMO. How it works and how powerful it is. This also makes it necessary to change penetration rules and introduce anti-magic rules, so to speak, for passive, proactive and reactive magic defense.
Stats etc
Change characteristics, more skills (especially for combat, it shouldn't be an easily learned hobby for magi to master), skill-groups masters in a given field might get a boost from, add/remove/balance virtues and flaws, introduce an endurance system to complement Fatigue: can be used for special maneuvers in combat and spontaneous spellcasting. Change Confidence.
Sorcery
Nerf ring duration (only wards), introduce a range between Voice and Sight, make several (we use 3) Arcane Connection ranges up to unlimited, reintroduce permanent duration, differ between creating something from thin air and healing/enhancing something. Remove minimal level for rituals and maximum level for formulaic spells. adjustment to Muto and Rego, including a nerf to crafts with Rego magic. Rules for natural resistance against spells: when you have it and guidelines for how hard it would be to resist. Change Form bonus. Rebalance some spell guidelines.
Change rules for warping and introduce temporal warping, remove that you can invent spells specially made for you so you sidestep warping. Change the Twilight system. Make familiars less of a magic item and closer to the idea of the third edition. Change the system for certĂĄmen, reintroduce the skill and add techniques for Tremere and those serious about it.
Study related
Change how books are written so people can improve writing, let books covering the same skill/Art boost each others Summa so a library of for example law books is even better then the best of the volumes in the library. Tractatus should be changed (we don't know how yet and have several different ideas). Introduce rules for using experiments to study.
Meta
Start from scratch if books about the infernal, dominion and the magic realm should be written.
Other stuff
New economy system, remove powers from priests: they should not be holy spellcasters. Maneuvers characters can learn and use in combat, fine tuning weapon stats. New rules for building laboratories. A new system for hermetic discoveries to make them harder and more special.
I would probably have optional rules for more cinematic combat online (if at all), using normal playing cards in a system that offers variation and tactic. We have not used it in Ars but in other games, works great for flashing blades kind of games. Either way, combat should not be the hobby thing it is now and turned into a real investment grogs and companions can master but magi seldom wants to waste their time with.
In my next campaign (if I GM another one) the Order would be the Hermetic Order, a timeline where Tremere succeeded and centralized the power. The Order would have a proper political system, taxes collected and used for the common good, some Houses would get a new purpose and roles (Mercere and Guernicus), etc. A more high fantasy setting where the Order and Byzantine joined forces and ushered in a new golden era of high culture, magic and technology.