Most of the known military figures of that period did not demonstrate a needed combination of the administrative and political qualities needed for staying in power as opposite to being just a figurehead. Of course, the problem with a figurehead position would be obvious: unless he is a complete idiot, sooner or later that person will became annoyed with the fact that after inducting the coup he ends up without any power which is being grabbed by the civilians like Syies. If he is still popular among the troops, these civilians are easily removed leaving him in charge. After which he, due to a complete incompetence in the issues not military makes a mess out of everything with the unpredictable consequences.
So what do we have realistically by the 1799?
Syies - intrigant with an excessively high opinion regarding his own mental capacities and no clear record of being a good administrator, diplomat or anything else. When given an opportunity, wrote a constitution that was complicated and lacking the basics (see recent thread about the re-elections of the consuls).
Moreau - the best general of the Republic. In conflict with the Directorate (hence support of the OTL coup) so seemingly suitable figure. Even better, no political ambitions whatsoever and sincere wish to enjoy the life and hunting. However, rather sensitive to the issue of a military glory (hence OTL conflict with the 1st Consul) so he would hardly willingly abandon the military career and, being a formal head f the state, he could deal harshly with those responsible for the problems with supplies, etc., which means inevitable conflict with the civilian government.
Massena - 2nd most reputable general. No known political ambitions, no administrative abilities to talk about. Great tactician but not a strategist at all so it is not clear if he could handle the “grand strategy”. Leaving it all to Syies? Stingy and greedy to a somewhat indecent degree (no item was too small to steal

) which was damaging his reputation among the colleagues. Hard to say how this combination may work out in a long term, especially in a country which needed “law and order” regime.
Joubert - IIRC, was expected by Syies to be his “sword” but had been killed. Acted mostly in the subordinate positions and there is no reason to assume that he would be willing to play a clown doing Syies biddings: in 1798 he resigned his position due to a conflict with the civilian authorities so how about him, being formally a head of the government, ordering to execute these “authorities”?
Thomas-Alexandre Dumas. The divisional general with a successful experience of army commander (Army of the Alps). Handsome and dashing to an extreme and very popular among the troops. No known political ambitions, administrative capacities. Seems to be rather hot-tempered (quarreled with Nappy in Egypt) and as such potentially dangerous for the people like Syies. The interesting twist is him ending up as a founder of a French dynasty: Alexander II and Alexander III could be very interesting monarchs (if they do not give up their main occupation). With a benefit of a hindsight, would be the most politically correct figure possible: just imagine mulatto as a head of an European state in the early XIX.
Bernadotte. The only (besides Nappy) military figure of that period who had military, administrative and diplomatic skills
proven by the time in question (unlike Nappy, his idea of a diplomacy was not limited to the bullying). Reasonably popular among the Republican military but, as the future events demonstrated, quite flexible when it came to his personal ambitions. Moreau’s friend, which could come handy. The main OTL problem was that sometimes he was more concerned with screwing up others more than with promoting himself (hence his neutral position during Nappy’s coup). Notwithstanding the ambivalent personal relations, Nappy could not afford not to make him a marshal. Based upon his experience as a governor of Hanover and later in Sweden, probably the best candidate.