We present a detailed study of the phase diagram of copper intercalated TiSe$_2$ single crystals, combining local Hall-probe magnetometry, tunnel diode oscillator technique (TDO), specific-heat, and angle-resolved photoemission spectroscopy measurements. A series of the Cu$_x$TiSe$_2$ samples from three different sources with various copper content $x$ and superconducting critical temperatures $T_c$ have been investigated. We first show that the vortex penetration mechanism is dominated by geometrical barriers enabling a precise determination of the lower critical field, $H_{c1}$. We then show that the temperature dependence of the superfluid density deduced from magnetic measurements (both $H_{c1}$ and TDO techniques) clearly suggests the existence of a small energy gap in the system, with a coupling strength $2Delta_s sim [2.4-2.8]k_BT_c$, regardless of the copper content, in puzzling contradiction with specific heat measurements which can be well described by one single large gap $2Delta_l sim [3.7-3.9]k_BT_c$. Finally, our measurements reveal a non-trivial doping dependence of the condensation energy, which remains to be understood.