Is there some better alternative to phrase
as well as for an academic writing? It sounds to me too informal.
The whole sentence is:
Improvements of both parts are possible as well as joining them into one piece of software.
The sentence, as is, does not indicate any real relationship between the 2 options other that both exist. A conjunction that showed a preference or a conditional relationship might add to the meaning and resolve your wording issue.
How about "While it is possible to improve both parts, the two can also be joined into a single piece of software." Or "The two parts may be addressed separately or may be joined into a single piece of software."
"and so is" may fit better into this sentence, so the new form would be:
Improvements of both parts are possible and so is joining them into one piece of software.
A better way to express that, though, is as follows:
Improving both parts is possible and so is joining them into one piece of software.
The two softwares can be individually improved, or made to work more cohesively as a unit.
Phrasing it this way allows for the softwares to be more integrated or re-written as a single piece of software. Monolithic architecture can be counter-productive unless the refactoring produces better modularity. But that's just me waffling on now.