I've come back to Medieval II after several years and re-downloaded the mod, which I found just as enjoyable.
However- I did feel that the map does have one major issue- Scandinavia is grossly over-represented province-wise and it was bothering my history geek enough to post.

Medieval demographics are always tricky, especially given that we're talking about a couple centuries, but some general ballpark estimates are available via Wikipedia.
Broadly, Scandinavia had about 300-500 thousand people in it. For comparison, Italy had 8-12 million, France 10-15 million, Hohenstaufen Sicily had around 2.5 million and England had about 1.5 million at the Norman Conquest and close to 4 million at the end.

Scandinavia+Finland has 10 provinces: two Norwegian, two Danish, and 6 rebels. England+Wales has 6; Italy as a whole has 12; and Southern Italy has 4. This is a respective population/province ratio of 30K-50K, 625K, 667K-1000K(!), and 250K-667K, respectively. In brief, Scandinavia needs many fewer provinces and Italy (especially Northern Italy) needs more.

My suggestion would be to remove all current rebel provinces save one for Sweden+Finland, and making Denmark and Norway both one-province factions, with Skane/Greater Gotland now held by rebels. That frees up 7 new provinces and still leaves Fenno-Scandia with an anachronistically large 4 provinces (75K-125K) for a population a fifth (or even a tenth!) that of the contemporary Kingdom of Sicily.

As to what provinces should be added instead:

ITALY

It made little sense to cut Genoa on a strictly faction-based analysis. Pisa in the first place is basically a reskinned Genoa, which was a reskinned Milan- the Milanese roster made some sense for Genoa but not for Pisa, and Pisa probably should get her own (Marines or Sardinian Skirmishers?) units anyway. In any event, Genoa was a major player- certainly larger than Norway!- and there are two free faction slots available, so why not add them? The only issue is the lack of provinces for the factions to fight over, and that now can be fixed. Italy's got 1 province each for Venice, Pisa, and the Papacy, three for Sicily and 6 for rebels, for a total province count of 12 provinces. I strongly suggest adding two more and am favorably inclined for four.

The first province that should be added Pescara (Rebel castle) carved from southern Spoleto and northern Apulia, a natural target for Naples; Ancona would then be switched to a city. Historically Naples did eat part of the defunct Duchy Spoleto shortly after the startdate, and this would hopefully bottleneck them a bit from meandering up towards Bologna every game. Ancona meanwhile was an independent republican city state that defied the rule of the Pope (and the Emperor?) and occasionally rivaled Venice for the Adriatic; it should probably be stronger/more valuable than it currently is. Italy having lots of cities is historical, after all.

Presuming Genoa is included again, we need another province in the north for her to fight over. My tentative suggestion would be either Lucca or Modena (castle) in the province of Emilia, between Lombardy, Romagna, and Tuscany as a bit of a buffer. Other province suggestions are Turin or Brescia/Bergamo (or both?) carved from Lombardy, Siena carved from Eastern Tuscany, Urbino carved from Marche/Romagna, or Aquileia carved from Venice.

FRANCE

France is also desperately in need of provinces, given her size and importance. I suggest at least two- a city of Narbonne (or perhaps Montpelier?) in Septimania along the southern coast, and a city or castle of Arras/Artois/Calais just south of Flanders.

Other possibilities include Hamburg to give Denmark and Germany more to fight over, a province (Vladimir?) in Russia between Kiev and Novgorod, a province in southern Anatolia- presuming that the final faction slot is used on Cilician Armenia- or more provinces for France or the HRE. I am interested to hear any suggestions or feedback, since I do intend to make a submod implementing the above.