"Ukraine had an NGO driven bloodless coup (kind of). This coup was clearly the doing of the U.S. ... The CIA appears to have a record of incredible incompetence"
That is not so, not quite, and that deserves some elaboration.
♦ The CIA just doesn’t do coups anymore
Of course, Bush 43 authorised the CIA do do destabilisation missions in Iran to achieve regime change, so take that with a grain of salt. But today, regime change is largely run out of the State Department. In the 70s, the CIA's history of coups and regime change caught up with it and was met with a public backlash that culminated in the climatic Church comittee hearings.
The politicians who wanted to keep doing these things irrespective of that moved the programs out of sight, and shipped staff and shop over to other organisations and found new sources of funding.
Lest these programs be again interrupted through pesky "oversight" by elected representatives, the new venue needed to be outside the bodies of the executive branch. The solution was government funded NGOs in the mold of Germany's Parteinahe Stiftungen.
♦ Regime change à l'américaine is a group effort now
Today, to the extent they concern 'soft power', such activities are run by the State Department through surrogates - semi official (USAID, NED, NDI, IRI, CIPE and ACILS), contractors and public relations firms or (congenially) entirely private (Soros' Open Society Foundation) and professional activists (OTPOR veterans). This is being supported by sympathetic journalists (providing friendly coverage or joining the fight) and pundits, lobbies (especially the transatlantic ones - Marshal Fund, Atlantic Society etc.) and think tanks (think Freedom House etc).
The semi-independent 'NGO' character of USAID, NED, NDI, IRI, CIPE and ACILS guarantees continuity in the democratising mission even with changes in government. The diverse ideological thrust of each organisation also addresses different different segments in the society of "to be developed" countries. It also provides plausible deniability. Also, these programs may be run by genuine idealists, who are not serving the US government, let alone the CIA, and will not think of themselves that way.
A lot of US support to Poland's Solidarity movement during the Cold war went trough the AFL-CIO linked ACILS, who apparently were far better connected than the CIA.
In a nutshell, these bodies run their various programs autonomosly in a decentralised fashion. In the absence of intervention, they do so on auto-pilot in accordance with the bipartisan consensus (on regime change in Russia, Cuba, Venezuela etc pp), much like on tram lines - and they may not get every memo.
A perfect example for that is the recent case of USAID vs. Cuba in which USAID sponsored a free twitter-ish program to organise resistance to overthrow the Castros - while the US administration at the same time pursued normalisation with Castro's Cuba.