I have a Scott Speedster 30 Aluminum bike 2016 with 10speed Shimano Tiagra Flat pedals stock wheels...
I seek advice What reasonable upgrades can I make and benefits
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As stated in comments on the question, there is a duplicate question that has a number of good answers. This answer will focus on one item, because the OP specified that he has flat pedals on a road bike.
All serious road cyclists will benefit from clipless pedals. I believe the same is true of nearly all gravel and many mountain bike cyclists. Clipless pedals enable you to pull up as well as push down with your feet. They really are a noticeable improvement to the ride.
Common concerns are that there is a learning curve. If you are using road clipless pedals, most riders fall down once or twice while stopped, as I can attest. However, you don’t have to use road clipless pedals (e.g. the Look Keo or Shimano SPD-SL), even though you’re on a road bike. Road clipless pedals usually have lower stack height than MTB pedals, and they do have a bigger platform. These may improve power transfer. However, if you have shoes with a stiff carbon sole, the issue of platform size may not be an issue.
In general, some riders may worry what happens if they crash while clipped in. I can report that you will almost always un-clip involuntarily as you fall. This has been true for me on both road and MTB pedals. I bet most of my fellow cyclists have crashed at some point (hopefully minor crashes!), and that they will report the same.
Mountain bike shoes are unquestionably easier to walk in than road bike shoes. MTB pedals and shoes may be a significant boon for many cyclists, particularly tourers or commuters. However, road cleats are not impossible to walk on. Rubber cleat covers are available for many cleats, or some cleats have integrated rubber bumpers.
For most road pedals, there is the complication that you have to flip the pedal slightly as you clip in. Many pedals are weighted such that you don’t have to flip the pedal as far. Alternatively, Speedplay pedals are double-sided. That said, I would recommend that most newer cyclists stay away from Speedplay, as the pedals and cleats need more frequent maintenance and the cleat setup can sometimes be tricky. (That said, I exclusively ride Speedplay on my road bikes.)
I have minimal MTB experience, but I understand that some mountain bike disciplines may favor flat pedals, as they are on very technical terrain and it is advantageous to be able to put a foot down occasionally. Some adventure cyclists (I.e. gravel bikes on very technical terrain) may also be in this position.
The best upgrade is the one that solves a specific problem or replaces a worn out part. Changing out any part on your bike should be done with a goal in mind. Your goals should be determined by identifying some specific way your bike could work better for you based on your riding style, terrain and personal goals. A "good" upgrade for one person could be a terrible modification for you.
Based on this premise you need to evaluate what specifically disappoints you about your bike? Here are some examples:
Once you identify the need, or the goal you can ask a specific question and gain specific answers. The other benefit is that you can know if the change you made met your goal.
For a 2016 bike first thing to do should be replacing "spesific urgent needs" as mentioned in another answer.
Then I would check the parts with operatonal life time and replace if they are expired. Few examples are;
When you have a solid bike without any broken or diminished part, you can start to replace other things. When you are doing that you need a main targer such as;
Lower bike weight
More aero gain
Or few of them together. So this is the main path for doing some changes for 4 years old bike I believe.