Why isn't government divided in some other way (e.g. there could be financial branch, internal affairs branch, etc.)?
Who decides what is what? For example, if a bank bribes a government employee with money collected illegally. Is that investigated by the financial branch or the internal affairs branch? What if both claim jurisdiction? Or neither? Who decides?
Note that this is problematic even in the traditional separation, which is much clearer. In the United States (US), the executive writes regulations, which are effectively laws--the province of the legislative branch. The legislature writes explicit instructions for things like the timing of traffic lights funded by a spending bill--the province of the executive branch. The judicial branch writes decisions that explain what is and is not legal, establishing standards used in other cases--the province of the legislative branch. The legislative branch gives arbitration powers to the executive branch--the province of the judicial branch.
The advantage of the traditional separation is that each has certain things that only it can do. Only the judicial branch can adjudicate law suits. Only the legislative branch can write the original laws. Only the executive can hire police to enforce laws outside the legislative and judicial branches (which have some ability to police themselves). Neither the legislative nor judicial branches can order the military to do things. They can only restrict. The executive can order the military but is subject to legal restrictions written by the legislative and adjudicated by the courts.
The executive can enforce laws differently than the legislative expected. If the judicial agrees with the legislative then the executive either complies or is out of bounds on the law. If the executive is out of bounds, the legislative can impeach and remove the head of the executive. Or if the judicial agrees with the executive, the legislative can change the laws to match what it thinks should happen. That's what we mean by checks and balances.
Separating by topic causes issues. Note for example that the Homeland Security department in the US originally came to be because the Federal Bureau of Investigation (FBI) and the Central Intelligence Agency (CIA) were restricted from each other's purview. The CIA can only act in foreign countries. The FBI can only investigate domestically. But terrorists could come from foreign countries and act in the US. The cooperation between the CIA and FBI was weak in that situation, and neither was fully responsible when they failed. Each could blame the other and be at least partially correct.
In that case, both were part of the executive (as is the new department), so at some level they all were part of the same organization. What if there was a domestic executive and a foreign affairs executive? Then someone else would have to decide. That someone else would have to have a lot of authority over the other two. What would be the check and balance on that power?
Perhaps there is an answer, but it's not obvious what it might be. So countries stick with the tried and true separation of powers with the established checks and balances.