Rectifying failed MCU crystal oscillator design
If the crystal is oscillating at 25MHz then your apparent problem is elsewhere, perhaps configuration of the clock divider, PLL or whatever that particular chip incorporates. Make sure your measurement is not affecting the oscillation.  

None of the items you mention are likely deal killers. It’s quite normal for the voltages at the crystal to be small relative to the supply voltage, even when properly measured with a FET probe.  

Sometimes a series resistor is even used to reduce the drive in order to avoid damaging the crystal with excessive drive power, especially for small SMT crystals that are limited to 100uW or less drive.