So let start with MIDDLE MAN:
-SNIP
So Bob here is the middle man, he can affect time of transaction and especially if he go offline.
The time is not a real problem since every transaction has its own timeout. It all happens nearly instantly. I have sent about 100 LN payments and the longest one took 1 minute. Bob can't steal funds because of HTLCs
LN is a network of several centralized hubs ... and you have to choose a performent and all time online to prevent delaying transaction etc ... So here a contract of trust ...
You can still open a direct channel to someone who you are going to transact with very often.
Here you can see the largest nodes. Only one node has 1/4 of the total Lightning Network capacity. Keep in mind that principal is not the most important factor; the number of connections and channel balancing are much more important. The need of being online is definitely a huge disadvantage for some people, can't argue with that.
Colluding miner attacks - miners have power to decide which transactions they want to include in the block so they can refuse certain transactions selected by an attacker. This attack is very unlikely to happen due to high cost and complexity (all miners would have to cooperate).
You have to trust miners.
If ALL miners decided to cooperate with a single person then you would have to be more concerned about 51% attack. It won't happen since it would scare future investors and users. Miners would lose money long-term.
It took me some time to format this text on my phone. I am going to read what you have linked once I get home.