2. Where to put big junctions: Squares are rare magnets, so giving every line access to at least one square prevents square-bound riders from piling up on transfers. My "major" hub is usually a square near the geographic center or a bridge choke, and I try not to merge too many trunks into one block-split load across two nearby interchanges if possible. If you have special shapes (stars, etc.), connecting each special to exactly one line that meets others only at an interchange keeps flows predictable.
3. Crossing lines away from stations: It's not catastrophic, but on busy trunks the cumulative hit adds up. I'll avoid mid-block crossings on high-throughput segments; elsewhere I don't contort the whole map just to eliminate a single crossing. Net: treat it as a tax, pay it only when it saves tunnels or ugly detours.
4. Random station getting swamped: Triage in this order: turn it into an interchange (boarding speed), add a loco, then a carriage on the most burdened line, and only then re-route another line to cross it. If nothing stabilizes, drop a short "shuttle" micro-line from that station straight to a square/triangle sink, then delete it once the queue clears. Pausing to redraw aggressively is part of the game.
On those early "beginner's luck" highs: seed luck is real but also the game rewards ruthless mid-game rebuilds more than early cleverness. Don't be sentimental about lines-pause, re-lay, and keep every line touching a square.
I have not heard of or seen a secret level!