There are many many threads, but none that really describe what to do to successfully get a Suzerain off your city. After getting two of my cities colonized from a sneak attack while away, I dove into this with everything I have and successfully got both of them back. It took 2 weeks to do so, but I did it, now you can too.
First you really need to be in an alliance, if you aren't, find one that will take you in. If you have only one city, this will be tough to overcome, but still possible. I will start with you, the one with only one city and what you need to do.
Single City Player
Keep your production up, you need the resources, shutting everything down will never get you away, the Suz still gets 15 of all resources, and depending on population, gets 10% of gold too. With everything at 0%, there is still 100 production from the fields, and a small tax for gold. Another thing to consider, you have a protector now, he has to do all your defences for your city, so it isnt too bad a deal. You could declare war on a much larger player, and have that player attack you, in which case, he may take you over instead, and depending on the player, keep or release you. The best thing to do though, is to win an uprise and free your city altogether.
If you get an alliance, see if a member close by you can garrision your troops while you are away. When you are online, get them going farming valleys, and NPC's. Train your troops, you will need troops in order to uprise, but while away, keep them away from your city, either camp them on a valley you own, or garrison them in a members embassy. Have alliance members send you resources. A Suzerain cant take what you have, only what you produce.
If you can, follow the quest to get Knight status, this allows you to build a second city. Now you have 2 options, build the second city nearby, send your troops to it, and when ready, uprise, OR, disassemble the first city, provided the TH isnt very high, IE lvl 10, (you cant get that back), then once you have everything down to lvl 1 or gone, abandon it, after the next server reset, the city will be removed, the Suzerain loses it.
You have a better situation here, you have more cities to use against the Suzerain. In this case, you can shut these cities down, when you do, your idle population goes up to max, especially if you applied Comfort to remove the greivance. You can send resources to this city, and train a LOT of troops, preferably archers, and once trained, move them out, dont let them sit there, the Suzerain can draft 10% of them. Dont stop upgrading either, keep building up the fields and buildings. Even out the number of archers and warriors in your other cities based on your rally point and distance. You will want to be able to send them all in large groups with perfect timing, as you will see later.
When you uprise it is your troops against the Suzerain. There is a percentage set on each colony of how many troops a Suzerain has for suppresion of an uprising, some may be 0, some may be 100%, depending on how valuble the colony is. It is this percentage that you are going up against. To get an idea how many troops you will be facing, you need a sacrificial amount of warriors. Get about 500 of them in your city, and go to your Suzerain, and click uprise. You have 2 ways to do this, first is on the map, if you know where it is, you can click on the city, and click the uprise button, or if you hold your cursor over your city picture on the right of the map, you will see a box pop out, click on it and you will have the option to Uprise, or commision an uprise. Click on Uprise. You may want to do this a few times to get the variables and to see just how the other player is using his troops.
Now here is the important part, one I myself failed to do and had to wait another week to free my second city.
OPEN YOUR GATES!
Click on your rally point and check the box open gates to fight. If this is not checked, your troops will not fight.
Let the uprise finish, and you should get a report back showing the Suzerain troop strength. This is what you have to counter when you are ready to actually uprise. The goal is to have more troops than he does. The best troop is of course Archers. Just make sure you have more archers than he does, not more warriors. You can have 300K warriors, and he may have 100k archers, you will lose. For a successful uprise, have archers and warriors, at least 10-20% more than he does, and you will win.
One thing to remember, it is your troops against his. Troops, not wall defenses, they do not play a part in an uprise, don't let anyone tell you different. None of my battle reports showed any wall defenses, just troops. If you look at a battle report against a city you colonized, or an NPC, you will see wall defenses in the report, but you don't see them in an uprise.
To catch the Suzerain off guard, uprise often, keep your gates closed in case you have troops you dont want to lose. He will never know when the real uprising takes place, and eventually he will stop trying to hold back his troops, thinking you are bluffing, then when he least expects it, POOF he no longer has your colony.
When you are ready, and feel you have enough troops to over power his and gain your city back, click on the uprise, keeping in mind that in 7 hours 55 minutes you need to be online ready to make your move. During the uprise, if your Suzerain is online, he may scout you to see if you actually have any troops, and prepare accordingly, he may also apply draft or disarmament policies druing this time, so if your troops are there when he does, you will either lose troops, or not be able to fight. This is why you want to uprise often, to throw him off gaurd, at some point he will ignore you, and increases your chances of winning.
You will need to time this perfectly, the ultimate goal is to have ALL your troops in the city during the last minute of the uprise, so first see how long it takes to get all your troops into the city and do this ahead of time so you know. When the time comes Send in the troops. You will also want to make your highest attack hero the mayor during this time, as the Mayor is the one doing the uprise. If you have any alliance members willing to reinforce you, make sure your Embassy is at least lvl 4, and have them reinforce you during the final minutes of the uprise.
After you WIN
If you are in an area that is far from other members, and close to the Suzerain, try to teleport away from him AFTER you have uprised, NOT before. Teleporting does nothing to rid you of a Suzerain, so dont waste it while colonized. Using it after breaks his hold on you for good, since he wont know where you went, and reduces the chances of him retaliating and trying to get you back. If you can use an Advanced Teleport, try to get into a cluster of alliance members for better protection.
Hope this has helped you like it helped me.