The main problem here is that both desire expansion in the same places - North America (because colonialism) and the East Indies (because money and spices (thus money)).
They are going to be rivals, and war between the two is extremely likely. Trade monopolies were just too tempting, and sometimes required military force to maintain.
Maybe the Netherlands accept Cromwell's invitation to unify with the Commonwealth?
All true, but the problem will always remain that the Netherlands wanted their independence, joinging with the Commonwealth would require both governments to agree to a unified system (I can't see Parliament and the Netherlands system co-existing very well).
In any manner that gives a reasonable balance of control, the English Commonwealth would control everything - if the Netherlands adopts a Parliamentary system, short of an ideological marriage, the English MPs would outnumber the Dutch. If you did it by the Counts - then the English equivalents would outnumber the Dutch. I can't see the Dutch being willing. Not without some decentralisation/veto clause.
What you would be more likely to succeed with is the "Joint Dutch and English East India Company" - where both the Netherlands and the English enjoy equal ownership. Having them both working together would create a trade juggernaut - to both sides benefit. Dangling this in front of the Dutch, or offering to base such a company under a unified Anglo-Dutch Commonwealth in Holland may be the best way to achieve a union. Especially if the board that runs said company is made up (initially) of equal members English and Dutch (specifically the Dutch Statholders)
Having an Anglo-Dutch Raj and Anglo-Dutch Indonesia is an interesting idea.
Oddly enough, the OPs desire is the best way to achieve the unity that they want.