Basically, MKJ's AI has a 'problem' when a lowertech AI attacks a highertech AI's fortress in a province with low supply levels.
The AI calculates the 'maximum' number of troops they can send to seige the fort when supply is factored in so they will not loose too many men due to attrition (which Paradox's AI is riddled with). However, certain forts require a certain minimum number of troops or else they are forced to retreat. I believe that tech differences require a certain increase of troop numbers to seige a fortress owned by an empire with higher land tech. For example (not based on fact, but theory).
To seige a small fort
Tech levels are equal...
Attacker needs an army value of 10 or more to continue the seige.
Tech levels are in favour of the defender of the fort...
Attacker needs an army value of 15 or more to continue the seige.
This is not really a problem until troop maximums determined through supply are calculated. If supply will only allow the AI to send an army value of 10, but needs an army value of 15, the troops will be continually sent, forced retreat, sent, forced retreat, sent, forced retreat, etc... until peace is declared. The poorer tech nation can only be off by 4 or so tech points (easy to occurr in the 1500's) for this to occur.
However, I have only really seen this occur twice in my games using MKJ's AI with EEP version 1.1a, 1.2 and 1.2.1. Once with France trying to take over the last base of Burgundy, and another time with the Ottoman Empire trying to take over the Venecian island provinces (in 1.2 the Ottomans repeatedly did not have trouble keeping up with the rest of Europe).
There are many possible solutions to this problem.
#1. Increase province supply minimums in certain bases to allow for realistic instances in certain bases of seiges occurring between larger and poorer tech troops against smaller higher tech forts.
#2. Lower some of the starting fortifications. I personally lowered Venice's forts in the Greek Islands to minimal, but this is a personal change.
#3. Find a way to change the minimum seige requirements so troops will remain at a base to seige it without being forces to retreat (although the seige will take an extremely long time).
I do perfer MKJ's AI to Paradox's AI, as the problems of Paradox are epidemic and occur throughout (such as attrition causing the AI to be a poor opponent as they kill of their own armies). It makes almost all wars very easy to fight against an AI opponent, and basically results in the nation that has the greatest manpower (so they can raise the most troops to replace the losses due to attrition).
MKJ's AI runs into problems due to too few troops to secure larger forts. However, there are possibilities that things can be changed so as to fix this problem if it epidemically occurs in certain situations.
However, this is a personal opinion, so don't take my word on this 100%. It really is a matter of a tradeoff between the problems and benefits of the two AI's, as well as your ability to try and personalize your scenarios as to match the AI you are working with.