The temporary reintroduction of border controls has nothing to do with France and Germany making their own exemptions, but rather it's a built-in part of the Schengen agreement, which allows for borderless travel.
FYI, this mechanism was used several times in the past, so it's nothing new and applies equally to all Member States in Schengen.
Regarding your assertion, Germany and France may have the biggest influence within the EU, but the EU is structured to ensure that the smaller Member States' interests are heard. Decisions are made with unanimity (core policy areas, any MS can veto) or QMV (other areas, calculated with formula to ensure it reflects more than a majority of states and EU population) so that decisions are sound.