Presently, acid-base reactions are almost entirely manual and this can cause some issues (for example, neutralizing weak acids) along with general unrealism.

A solution to this would be the ability to give molecules and groups "acidity maps", basically marking a proton and saying "this has a pKa of x". This would allow deprotonation to take place similar to how they happen irl.

A good way to implement this would be starting with the most protonated form of the molecule/group and marking a proton with a pKa and either marking a different proton on it with a much higher pKa or instead mark a proton on water with that pKa (I do not know which would be easier to code).

In addition, there should be a way to manually exempt individual molecules from generic pKa values, for example formic acid having a much lower pKa value compared to most other carboxylic acids and acetylene being the only alkyne with two protons with one being far, far higher than the other.

Bases would not be looking for loose protons but instead looking for acidic protons on molecules. They would then compare their pKa values as they do irl and depending on the value decide to deprotonate or note, just like real life!

One problem is that there are so many things with a pKa. Every alcohol, amide, carboxylic acid, etc. A good band-aid solution is to give every group a pKa and not to worry about how the rest of the molecule effects pKa.