The fact that they have thousands of ships but only have 1 or 2 ships guarding there most vital planets! Fix your defences!
If you think about it, Earth is probably better defended than it might seem at first glance. TMP said that V'ger deactivated Earth's defenses, so it might not in that case have been that Earth was undefended, just that Earth's defenses couldn't deal with V'ger's technology. It would have been a similar story with the "Whale Probe."
The Borg cube in FC didn't exactly approach Earth unopposed, the impression I got from the movie was that Starfleet was employing a defense in depth, and that they were fighting the cube over the course of certainly hours and perhaps multiple days. As ships were knocked out, new ones arrived to take their place.
The Breen (Breen?) attack upon Earth during DS9 damaged only one relatively small area and the attacking force was heavily hit themselves. The Breen force could have been attack on their way in, and this is why their attack was so "light."
You jokeing right?
The federation spans I believe afew hundred odd light years do you even understand how vast 1 light year is?
Picard say "over" eight thousand light years (althought that might be at it longest dimention). A good case could be made that Starfleet ships exist in the tens of thousands, problem is many of those would be unsuitable for combat.