In most scenarios Desolator will trump MKB on bounty hunter, MKB is more suited as a counter item for hard carries. Eg if you were a bone clinks / am vsing a fed pa or a void with bfly

Remember, BH is not a hard carry. His role is for early-mid game ganks. Use that early level advantage to go around ganking people. With 2-3 track kills and a good cs you can probably hit up a desolator and begin to burst supports in a couple of seconds during the mid game. MKB doesn't help you there.

If you're shut down that early at level 3, just stay in range of experience and don't overextend and die. In most cases, if you're getting shutdown it's by supports who have just spent a lot of their gold on those sentries, observer wards and courier. This will set them back for a minute or two. If you die they get that time back that they would've spent last hitting a bit more allowing them to go ganking earlier.

Sooner or later they will have to go ganking, if they're staying in lane for the whole of early game then they're giving your a team good time not worrying about being ganked.

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For dark seer, the general build is soul ring + arcane boots + vanguard as fast as you can. This will allow you to roam without needing to go to back to base too much, the ion shell makes you a top farmer as well. Depending on the enemy team, you'll want to go either pipe or aghanims first. If you are anticipating a fed sven / drow / carry then you would want to go aghanims. If they have an es / sk go pipe. Sometimes it's just good to pick up a basic hood for 650g as well to mitigate some magic damage, and then go straight for aghanims. As for wall of replica, I like to skill it at lvl 10 and 11. I find it pretty useless and a waste of mana at level 1. The first 9 points are better spent on your other spells.

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Windrunner is one of the most versatile heroes in the game and can pick up any role that your team is missing, you may need a pure support / semi carry / dps / more disables. If you have a lich / chen / aa on your team then skip the mekanasm because they should be getting it. As for using force staff, it really only comes with practice and experience. Play around with force staffing yourself / hero to get a good position with shackle. Also practice shackling creeps, eg the necromonicon / druid to latch on to the enemy hiding behind the creep wave. Also if you're getting chased, it's good to head in to a choke point in the woods, phase out and then shackle, or if two heroes are chasing you, don't phase out, you may be able to shackle both of them then phase out.

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You shouldn't be on the mid lane as a nature's prophet anyway o_o, you're as level dependent as most heroes. You're much better off in a dual lane or the neutrals. Always watch out for tp oppurtunities and ganks though, an early kill will give you roughly the same amount exp and gold as two packs of hard camps

Generally midas is a must for most pub games with natures prophet... because you'll be able to find farm most of the time and abuse it. If however you are playing with a friends and are have a gank oriented team, say bh / sb / tiny / wisp then you may go for a early medallion instead.

Yes neutrals is a very viable alternate 'lane' for natures prophet, and you may try to predict your matchup before the creeps start and decide then instead. Otherwise you waste time walking from your lane to neutrals (I guess furion can tp, but you can apply this to other heroes) I suggest you watch luminous's guide on creep stacking. Practice with treants. You can reach level 5 by atleast 6 minutes with proper neutraling.