We have forgotten that the "fund smart people and let them do what they want" is the best approach. Look at Xerox Parc, Bell Labs, etc. Nasa's modern approach with SpaceX and other companies seems to reflect these hard learned lessons.
One interesting piece of history (Chertok wrote about it in his memoirs) - in Spring 1961, just before Gagarin's flight, which, of course, was priority number 1, Korolev managed to worry about upcoming R-9 testing, saying to his people "after Gagarin, they won't allow us to work on R-9 as easily".
Korolev did enjoy significant freedom in how he did things - the Council of Main Designers was created thanks to that freedom, and von Braun's decision to add fifth F-1 to Saturn just because he felt it will be needed - bypassing all bureaucracy - would be quite understood by Korolev and his team, they had similar things done themselves. It was often the case that Korolev went to Kremlin with some space-related offerings, and got green light, after the principal work was already done, and more scaled-up development was all what remained. You have to work your asses off this way of course, but you have full support of your political bosses and you're a hero for everybody.
And in the USSR Glushko also played along initially, designing R-7 engines that are in use till today basically. Only later he stopped and started demanding all future engines to be hypergolic, which didn't go well with Korolev, especially for crewed vehicles.
I think Glushko owns a big share of Soviet problems with the Moon.
On the other hand, at the time the leading idea in USSR was that hydrogen is a rather advanced fuel (which, by the way, Glushko also supported at a time), and given good existing engines, rocket designers wished to use proven fuels. In general, and to compete with hydrogen in particular, Isp was an important goal, so rocket designers set goals to engine designers - make rocket engines with good Isp. There was created a conflict between high Isp/high pressure engines - as required - and large thrust engines, as was needed for big, Moon rocket. Glushko had the opinion that they won't have enough time to create large thrust high Isp engines with kerosene, only with UDMH/NO2 . Kuznetsov could only create relatively low thrust (1500 kN) high Isp kerosene engines, and those were late.
If Glushko tried, those engines could possibly work. At least Glushko experience with large thrust chamber of RD-270 helped later with large thrust 4-chamber kerosene RD-170.
This all changed with Lyndon Johnson taking over, getting rid of the Germans, introducing the well known inefficient NASA/gov-style management style known from the Shuttle era, and moved the technicians out of Alabama to Houston. This was the anti-modern democratic approach.
SpaceX simply went back to the old modern style, which worked well for the US and Russia.
The trick was not using smart people, but experienced engineers in control, and not fresh anti-engineer PM's out of college. Everybody can control a budget, esp. engineers, but only engineers can control engineering problems.