It's a delicate transition even when the civilians have actual full authority over the government (see: South Africa, or worse yet, Zimbabwe). But when Myanmar transitioned to the free elections which put Suu Kyi in power, the military specifically reserved a significant minority of seats in the legislature and maintained constitutionally-guaranteed independence from the civilian government.

On top of that, the military had been the only functional institution in Myanmar for over 50 years. During that time, there was no real court system, no free media, no private industry, and no significant educational institutions. Even before the military took over, the majority of the colonial government bureaucracy consisted of Indians that the British brought in with them, the vast majority of whom left with the British, gutting civilian institutions. The military controlled every aspect of everyone's lives. Their retreat from total control left an enormous institutional vacuum, with Buddhist monasteries left as the only nearly national stable institution (which has fed tensions with minority Muslim ethnic groups).

When I was working there a few years ago, people barely knew what the laws were for creating a corporation. No one knew how to verify who owned what land. The military suddenly allowed free press for the first time since the 1960s, and immediately a plethora of dubious publications sprung up to compete with the hilariously inaccurate government-run propaganda rag, the Light of Myanmar. People just weren't equipped to evaluate journalistic quality yet. So fundamental elements of a free society just weren't in place.

And the population was in many ways unprepared for democracy. Atrocious education and decades of propaganda make it difficult to rationally exercise democratic authority. Particularly when there are strong ethnic tensions, because the majority tends to abuse their authority to the detriment of the minority. Hence the ethnic cleansing of the Rohingya.

So Suu Kyi is left in a tenuous position. She can't allow dissent within her own party without risking fragmentation and a loss to a military-centric coalition. She can't let her own party run wild without risking unfettered ethnic cleansing and a military backlash/coup if their special privileges are revoked.

This latest move is disheartening for many reasons, but more than anything it is evidence of just how desperate the situation in Myanmar really is, despite whatever brief optimism grew out of the nation's partial democratization.

Those things take time.

If you don't execute everyone from the old regime, there are tons of rich people, executives, special interests, influential families, etc, that remain in place and are still important after the transition.

(The post-WWII Germany was full of ex-nazi hardcore sympathizers, and nazi executives and officials in all kinds of positions of power until the 80s or so). De-nazification (not the half-arsed, soon abandoned program of the same name [1]) was a big demand of younger germans in the 60s and 70s.

Now, if you do execute all important people from the old regime, on the other hand, you have now had yourself a taste of big corrupting power over others. And unless you kill every relative, friend, etc as well, you have a recipe for civil war and further bad blood between you and those that remained.

[1] https://en.wikipedia.org/wiki/Denazification

Civilian dictatorship, such an euphemism for "democracy"