Sharpness issue - what is the cause

How long have you had the camera? When did the sharpness start becoming a problem?
Has it slowly gotten worse?

I agree the focus appears to be terrible on all of these, but it actually looks like hand held blur from a really slow shutter speed. How slow was the shutter speed? Maybe the focus system in your 1000d has started to slip over the years, since it seems to happen on both lenses you have.

The lens is basically a free lens that was a a little soft wide open from what i understood, thing is, this lens and body are 15 years old and who knows what has happened to it. If the lens was jared it could have been knocked out of alignment, but if the images have slowly started to have focus issues over time then the camera may have something else going on with the focus system. Either way this gear at this age is worth maybe $30 if its in good working order, so an upgrade to both is probably a good idea given its value.

https://www.the-digital-picture.com/Reviews/Canon-EF-28-90mm-f-4-5.6-II-USM-Lens-Review.aspx

 

to me its a very simple both, neither of those lenses can be sold for anyhing, they are throw in the kit for free by canon lenses. The body is likely just loosing accuracy in the focus system over time.

Normally i say upgrade the lens keep the body to many people asking what to upgrade first, you always want to put the absolute best glass you can afford in front of the sensor.

In your case though this is an entry level camera from 2007 that seems has lost its ability for tight focus. I say this because both lenses seem to have the issue. Now to be fair both of these lenses are entry level lenses that also are 15 years old it seems. I would not feel like you lose anything starting all over here, but you can surely re use the lenses if you go APC again and see if they perform ok. That said, these are mediocre optically and would not replace them i would try to move up a step.

Lets start with a budget and an idea of what things you like to shoot and how you see yourself utilizing a interchangeable lens system.

I'll make an example: for me I primarily used film before going digital for landscape and macro so I invested in a 20d, back in 2004 and a 17-40 L and a 100mm Macro a year later. Both of those lenses were not dirt cheap lenses but would server me when i moved up to full frame which i imagines i would do at some point when i could afford since I like landscape and the full frame is more friendly to the wide angle side. Both these lenses are more ruggedly built than the plastic kit lens, the L is metal and weather sealed, both perform flawless almost 20 years later, a good lens is a long term investment.

 

Well i am going to go ahead and pivot after seeing that sharp image and assume the camera and lens MAY be ok. The test you did is missing some basic fundamentals in exposure.

Blur has nothing directly to do with your lighting via flash or you aperture you select.

Selecting f16 will instead of f2,8 will force you to find 5 times as much light some other way. Your pop up flash is not very powerfull and used only to help fill in shadows. This will force you to use a much slower shutter at f16 than f 2,8.

The Blur at a wide aperture like 2.8 or 4 is due to out of focus having a faster fall off if focus is missed, meaning 2.8 is not as forgiving as f16, a portrait at 2,8 is done at close distance and may have share focus in a small window of inches. A landscape at f16 done 50 yards away will have yards of in focus around the subject.

Your shot is indoors where lighting is not great and if your trying to stop down to f11 or f16 you are going to need a tripod.

Conversely you could crank up your ISO to 3200 or what every but it willl be very noisy especially considering the age of teh sensor. I can take images at 6400 easily with my 5d, better high iso performance will be very noticeably on a newer camera.. I never shot my 20d above 1200iso.

To test the sharpness of a lens itself, the sweet spot of usually around f5.6 to f8, there will be softness at the outermost edge of the glass as you get to the extreme ends, expensive lenses perform better.

TO TEST if you have an issue with focus, you need to also eliminate motion blur. Motion from being handheld you should shoot faster than the length of the lens unless you have image stabilization. So if your shooting above 1/100, that should eliminate this as an issue.
For motion from shutter slap, this usually creeps in between 1 sec and 1/4 of a sec . if you have a multi second image on a heavy tripod you should be good... If you are hand holding anything below 1/60 you will have soft images. Between 1 sec and 1/60 second is the worst range fighting blur, because you cant hold any camera and lens at 1/20 of sec without blur, and on a tripod especially one that doesnt dampen vibration well, you can get shutter vibration, but this is a small window and not a reason alone to go mirror less.

Shoot at at least 1/100 and you should be fine, you prob will have to shoot around f4 ish to get enough light to not crank up the ISO really high indoors. You are kinda close to the subject at times, the minimum distance to subject to even get focus is about 15 inches with that lens, i dont think that is an issue here but just saying there is a lot of math your not seeing happen here.

https://www.dofmaster.com/dofjs.html will tell you based on your focal length, f stop, and subject distance, how small of a window of fucs you are trying to hit with the focus system,

I still believe you should probably upgrade, idk if the focus system is inconsistent, but your one shot looks fine. And all the settings your playing with are not really telling much because i have no idea how slow the shutter is on every example your testing and if you were trying to hand hold it.

Newer camera with much better iso performance will give you some breathing room, a better flash instead of the weak pop up will help.
Paying close attention to the length of lens and shutter speed for freezing motion blur def will make a difference.

Now if you were testing your camera and lenses outside in daylight and getting lots of blur in image I would be more concerned that the focus system is shot, but right now i'm not convinced the gear is a loss, you have shot entirely close up indoors where the lighting is very poor. even the focus system can struggle in lighting that is poor. Especially such an old focus system. I do promise the gear is not forgiving when pushed to the limits.